Type:	Package
Title:	Next Generation Clustered Heat Maps
Version:	1.0.4
Description:	Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. 'NGCHM' allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) <doi:10.12688/f1000research.20590.2> for more details.
License:	GPL-3
URL:	https://md-anderson-bioinformatics.github.io/NGCHM-R/, https://github.com/MD-Anderson-Bioinformatics/NGCHM-R
Depends:	R (≥ 3.5.0)
Imports:	digest, grDevices, htmltools, httr, jsonlite, logger (≥ 0.2.0), methods, stats, tsvio, utils
Suggests:	knitr, rmarkdown, Rtsne, testthat, umap, uwot
Enhances:	NGCHMDemoData, NGCHMSupportFiles
Additional_repositories:	https://md-anderson-bioinformatics.r-universe.dev
Encoding:	UTF-8
RoxygenNote:	7.2.3
Collate:	'internalFunctions.R' 'allClasses.R' 'allGenerics.R' 'allMethods.R' 'functions.R' 'chmFromJSON.R' 'dendrogram-fixes.R' 'shaidy.R' 'ngchmshaidy.R' 'zzz.R' 'package.R'
SystemRequirements:	Java (>= 11) Git
NeedsCompilation:	no
Packaged:	2024-12-17 18:52:10 UTC; marohrdanz
Author:	Bradley M Broom [aut], Mary A Rohrdanz [ctb, cre], Chris Wakefield [ctb], James M Melott [ctb], MD Anderson Cancer Center [cph]
Maintainer:	Mary A Rohrdanz <marohrdanz@mdanderson.org>
Repository:	CRAN
Date/Publication:	2024-12-17 19:40:02 UTC

Next Generation Clustered Heat Map (NGCHM) Construction Library

Description

NGCHM provides tools for defining the contents of a new NGCHM, and for compiling and installing it on a NGCHM server.

Details

Typical usage (see example) is to create a base NGCHM using chmNew; extend it with at least one ngchmLayer; typically extend it further with an additional ngchmLayer, row and column dendrograms, classification bars, and popup menu entries; compile and install it on an available ngchmServer.

Note:

• chmNew() requires git to be installed.

• chmExportToFile(), chmExportToHTML(), and chmExportToPDF() require Java 11 and the NGCHMSupportFiles package. The NGCHMSupportFiles package can be installed with:
  
  install.packages('NGCHMDemoData',
repos = c('https://md-anderson-bioinformatics.r-universe.dev',
'https://cloud.r-project.org'))

Initialization

When first loaded the NGCHM library reads configuration files in the directories specified by the NGCHMCONFIGPATH environment variable. This is a colon (:) separated list of directory names. If not set it defaults to /etc/ngchm:/usr/local/ngchm:/opt/ngchm:$HOME/.ngchm. See NGCHM-initialization for details.

Author(s)

Maintainer: Mary A Rohrdanz marohrdanz@mdanderson.org [contributor]

Authors:

• Bradley M Broom bmbroom@mdanderson.org (ORCID)

Other contributors:

• Chris Wakefield cwakefield@mdanderson.org [contributor]

• James M Melott jmmelott@mdanderson.org [contributor]

• MD Anderson Cancer Center [copyright holder]

See Also

chmNew()

chmAdd()

chmExportToFile()

chmExportToPDF()

chmSetCollection()

chmInstall()

ngchm

Examples

# Examples using `chmNew()` require git to be installed.
# The NGCHMSupportFiles package is required by chmExportToFile and chmExportToPDF
# The NGCHMDemoData package is used to create a demo NGCHM
## Not run: 
  if (requireNamespace("NGCHMSupportFiles", quietly = TRUE)) {
    if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
      library(NGCHMSupportFiles)
      library(NGCHMDemoData)
      data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
      chm1 <- chmNew("gbm", TCGA.GBM.EXPR[1:50, 1:50],
        rowAxisType = "bio.gene.hugo",
        colAxisType = "bio.tcga.barcode.sample.vial.portion.analyte.aliquot"
      )
      chmExportToFile(chm1, tempfile("gbm", fileext = ".ngchm"))
      chmExportToPDF(chm1, tempfile("gbm", fileext = ".pdf"))
    }
  }
  mat <- matrix(rnorm(100), nrow = 10)
  rownames(mat) <- sprintf("ABCA%d", 1:10)
  colnames(mat) <- sprintf("Sample%d", 1:10)
  chm <- chmNew("my-chm", mat)

## End(Not run)

Provide a simpler method for accessing repo methods

Description

Provide a simpler method for accessing repo methods

Usage

## S3 method for class 'shaidyRepo'
repo$method

Arguments

Value

A function that calls the method with the repository as its first parameter

Add an Axis to an NG-CHM Version 2

Description

This function adds an 'ngchmAxis' to an 'ngchmVersion2' object.

Usage

## S4 method for signature 'ngchmVersion2,ngchmAxis'
e1 + e2

Arguments

Value

An updated 'ngchmVersion2' object with the added axis.

Javascript extensions for the Next Generation Clustered Heat Map (NGCHM) Construction Library

Description

Currently:

• Axis function View Ideogram is added for the appropriate axis types.

See Also

chmGetFunction()

chmListFunctions()

Initialization of the NGCHM library.

Description

When first loaded the NGCHM library reads configuration files in the configuration path specified by the NGCHMCONFIGPATH environment variable. The configuration path is a colon (:) separated list of directory names. If not set it defaults to /etc/ngchm:/usr/local/ngchm:/opt/ngchm:$HOME/.ngchm.

Details

For each configuration directory in the configuration path, the NGCHM package reads the contents of the configuration files in the conf.d subdirectory in order (as determined by the R sort function). Other subdirectories are not scanned unless instructed to by an entry in a configuration file.

Configuration files may be either text files (.txt extension), R scripts (.R extension), or javascript files (.js extension).

Here is an example directory structruce for a server named 'my_server':

.
|-- conf.d
|   \-- 00-servers.txt
\-- my_server
    \-- config.txt

Here are the contents of an example 00-servers.txt file:

[servers]
my-server = /usr/local/ngchm/my_server

Here are the contents of an example config.txt file:

serverProtocol = shaidy
accessMethod = api
basePath = <URL to server. e.g. "https://mydomain.edu/server/api">
serverURL = <URL to server. e.g. "https://mydomain.edu/server">

Value

None. This function is used for its side effects of loading configuration files.

Text files

A text configuration file consists of one or more sections. Each section begins with a single line containing the section type enclosed in square brackets. Subsequent lines in the section are either blank or contain a definition of the form "name separator value". The default separator is the equals sign (=).

The 'servers' section defines available servers. The name field defines the name by which the server is known to the library. The value field specifies a directory containing a specification of the server's properties. The server specification directory must contain a config.txt that contains lines of the form "name separator value". The config.txt file must define the value of 'serverProtocol' to be the name of a ngchmServerProtocol. It must also define the values of any mandatory parameters required by ngchmServerProtocol, and may optionally define any optional parameters.

R scripts

R scripts are sourced. They can be used to define local NGCHM related functions.

Javascript scripts

Javascript files define context specific menu entries.

Helper function to cast variables as integers.

Description

If variable value is far from integer, print error message and stop.

Usage

castAsInteger(variableToCast)

Arguments

Value

integer value of variableToCast

Helper function to cast list as integer

Description

If variable value is far from integer, print error message and stop.

Usage

castListAsInteger(listToCast)

Arguments

Value

list with members cast to integers

Add a list of objects to a NGCHM.

Description

Each additional parameter is added to the NGCHM according to its type. Objects that require additional information (such as an axis) cannot be added using this function. Objects that can be added are layers (including numeric matrices), datasets, and colormaps.

Usage

chmAdd(chm, ...)

## S4 method for signature 'ngchm'
chmAdd(chm, ...)

Arguments

Value

The extended chm.

See Also

"chmAddAxisType"

"chmAddColormap"

"chmAddDataset"

"chmAddLayer"

"chmAddMetaData"

Add an axis type to a NGCHM.

Description

Adds an axis type to a Next Generation Clustered Heat Map (NGCHM) and returns the extended CHM. Multiple axis types may be added to either axis. When the NGCHM is made, any Axis functions matching the specified axis type will be automatically added to the appropriate axis menu, and any Matrix functions matching the types of the rows and columns will be automatically added to the matrix menu.

Usage

chmAddAxisType(chm, where, type, func)

## S4 method for signature 'ngchm,character,character,ngchmJS'
chmAddAxisType(chm, where, type, func)

## S4 method for signature 'ngchm,character,character,character'
chmAddAxisType(chm, where, type, func)

## S4 method for signature 'ngchm,character,character,missing'
chmAddAxisType(chm, where, type, func)

Arguments

Value

The extended chm.

See Also

chmListTypes()

chmRegisterAxisFunction()

chmRegisterMatrixFunction()

chmRegisterTypeMapper()

ngchmAxisType

Add custom CSS to a NGCHM.

Description

Add custom Cascading Style Sheet (CSS) to a Next Generation Clustered Heat Map (NGCHM) and return the extended CHM.

Usage

chmAddCSS(chm, css)

## S4 method for signature 'ngchm,character'
chmAddCSS(chm, css)

Arguments

Value

The extended chm.

See Also

ngchmCSS

Add a colormap to a NGCHM.

Description

Add a colormap to a Next Generation Clustered Heat Map (NGCHM) and return the extended CHM. Duplicate colormaps will be silently dropped.

Usage

chmAddColormap(chm, colormap)

## S4 method for signature 'ngchm,ngchmColormap'
chmAddColormap(chm, colormap)

Arguments

Details

Note that it is not necessary to explicitly add colormaps included with data layers or classification bars. These will be included automatically. Explicitly using this function is only required in order to add additional predefined, but unused colormaps to the NGCHM.

Value

The extended chm.

See Also

chmNewColorMap()

ngchmColormap

Add a covariate to an auxiliary dataset.

Description

Add a covariate to an auxiliary dataset and return the extended dataset. Do not confuse this function with the one for adding a covariate bar to an NGCHM. For that, please refer to the function chmAddCovariateBar.

Usage

chmAddCovariate(dataset, where, covariate)

## S4 method for signature 'ngchmDataset,character,ngchmCovariate'
chmAddCovariate(dataset, where, covariate)

Arguments

Value

The extended dataset.

See Also

chmNewCovariate()

ngchmCovariate

Add a covariate bar to a NGCHM.

Description

Add a covariate bar to a Next Generation Clustered Heat Map (NGCHM) and return the extended CHM. If passed a covariate, a covariate bar will be created (using any optional parameters supplied) and added.

Usage

chmAddCovariateBar(chm, where, covar, ...)

## S4 method for signature 'ngchm,character,ngchmBar'
chmAddCovariateBar(chm, where, covar)

## S4 method for signature 'ngchm,character,ngchmCovariate'
chmAddCovariateBar(chm, where, covar, ...)

## S4 method for signature 'ngchm,character,list'
chmAddCovariateBar(chm, where, covar, ...)

Arguments

Details

If a covariate bar with the same name already exists on the specified axis or axes, the existing bar will be replaced by the new bar.

Value

The extended chm.

See Also

chmNewCovariate()

chmNewCovariateBar()

ngchmCovariate

Add an auxiliary dataset to a NGCHM.

Description

Add an auxiliary dataset to a Next Generation Clustered Heat Map (NGCHM) and return the extended CHM. The auxiliary dataset will be stored with the NGCHM and be available in whole or in part from the same server, for use, for example, in custom Javascript functions. Do not confuse this function with the one for adding an active data layer to the heatmap itself. For that, please refer to the function chmAddLayer.

Usage

chmAddDataset(chm, dataset)

## S4 method for signature 'ngchm,ngchmDataset'
chmAddDataset(chm, dataset)

Arguments

Value

The extended chm.

See Also

chmNewDataset()

ngchmDataset

Add an extra dialog to a NGCHM.

Description

Add an extra dialog to a Next Generation Clustered Heat Map (NGCHM) and return the extended CHM.

Usage

chmAddDialog(chm, dialog)

## S4 method for signature 'ngchm,ngchmDialog'
chmAddDialog(chm, dialog)

Arguments

Value

The extended chm.

See Also

chmNewDialog()

ngchmDialog

Add a Layer to a NGCHM.

Description

Add a Layer to a Next Generation Clustered Heat Map (NGCHM) and return the extended CHM. A CHM requires at least one Layer. The first layer added to a NGCHM becomes the primary layer. The second layer added to a NGCHM, if any, becomes the secondary (flicker) layer. Currently at most two layers can be added to a NGCHM.

Usage

chmAddLayer(chm, layer)

## S4 method for signature 'ngchm,ngchmLayer'
chmAddLayer(chm, layer)

## S4 method for signature 'ngchm,matrix'
chmAddLayer(chm, layer)

Arguments

Value

The extended chm.

See Also

chmNewDataLayer()

ngchmLayer

Add a menu entry to a NGCHM.

Description

Add a popup menu entry to a Next Generation Clustered Heat Map (NGCHM) and return the extended CHM.

Usage

chmAddMenuItem(chm, where, label, func)

## S4 method for signature 'ngchm,character,character,ngchmJS'
chmAddMenuItem(chm, where, label, func)

## S4 method for signature 'ngchm,character,character,character'
chmAddMenuItem(chm, where, label, func)

Arguments

Value

The extended chm.

See Also

ngchmMenuItem

Add MetaData to NG-CHM

Description

This function adds metadata to a NG-CHM (Next-Generation Clustered Heat Map) object.

Usage

chmAddMetaData(chm, where, type, value)

## S4 method for signature 'ngchm,character,character,character'
chmAddMetaData(chm, where, type, value)

Arguments

Value

An updated 'ngchm' object with the new metadata added.

Generate an overview image of the NGCHM when making it.

Description

Generate an overview image of the NGCHM when making it. By default, the system generates no default overview images. If only one of width or height is specified, the other is calculated based on the aspect ratio of the map.

Usage

chmAddOverview(chm, format, width, height)

## S4 method for signature 'ngchm,character,optNumeric,optNumeric'
chmAddOverview(chm, format, width, height)

Arguments

Value

The extended chm.

Add PCA coordinates to an NG-CHM.

Description

Add PCA coordinates as hidden covariate bars to an axis of an NG-CHM. One hidden covariate bar is added for each PCA coordinate (up to ndim coordinates). Coordinates are given names 'BASENAME.coordinate.N', where BASENAME is specified by the parameter basename (default "PC") and N ranges from 1 to the number of added covariate bars.

Usage

chmAddPCA(hm, axis, prc, basename = "PC", ndim = 2)

Arguments

Value

The NGCHM with added coordinates.

See Also

chmAddTSNE()

chmAddUMAP()

chmAddUWOT()

chmAddReducedDim()

Examples

# Examples using `chmNew()` require git to be installed.
## Not run: 
  # If the NGCHMDemoData package is installed, use it to demo usage
  if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
   data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
    prc <- prcomp(TCGA.GBM.EXPR[1:50, 1:50])
    hm <- chmNew("gbm", TCGA.GBM.EXPR[1:50, 1:50])
    hm <- chmAddPCA(hm, "column", prc)
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  prc <- prcomp(matrix)
  hm <- chmNew("Demo PCA", matrix)
  hm <- chmAddPCA(hm, "column", prc)

## End(Not run)

Add custom property to a NGCHM.

Description

Add custom property to a Next Generation Clustered Heat Map (NGCHM) and return the extended CHM.

Usage

chmAddProperty(chm, label, value)

## S4 method for signature 'ngchm,character,character'
chmAddProperty(chm, label, value)

Arguments

Value

The extended chm.

See Also

ngchmProperty

Add reduced dimension coordinates to an NG-CHM.

Description

Add (reduced) dimension coordinates from an object obj as hidden covariate bars to an axis of an NG-CHM. Depending on the object type, dimName and dimAxis can be used to specify the name of the dimension of interest in obj.

Usage

chmAddReducedDim(hm, axis, obj, dimName, maxDim, basename, dimAxis)

Arguments

Details

One hidden covariate bar is added for each coordinate obtained from obj. If specified, maxDim limits the maximum number of covariate bars added to the chm.

Coordinates have names 'BASENAME.coordinate.N', where BASENAME is specified by the parameter basename (defaults to dimName if omitted) and N ranges from 1 to the number of added covariate bars.

obj can be a numeric matrix, each column of which is a (reduced) dimension. In this case, dimName and dimAxis are not used for obtaining the reduced dimension. The number of rows of the matrix must equal the size of the specified NGCHM axis and each row of the matrix must be uniquely named using the names from that axis of the NG-CHM.

obj can also be an instance of class className if there exists an S3 method getDimensions.className. The method takes the object as its first parameter and up to two optional parameters, dimName and dimAxis, that can be used to specify the desired dimension. The method's return value is a matrix similar to the one described in the preceding paragraph. This package defines methods for classes prcomp and umap.

Value

The NGCHM with added coordinates.

See Also

chmAddPCA()

chmAddTSNE()

chmAddUMAP()

chmAddUWOT()

getDimensions()

Examples

# Examples using `chmNew()` require git to be installed.
## Not run: 
  if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
    data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
    mat <- TCGA.GBM.EXPR[1:10, 1:10]
    prc <- prcomp(mat)
    hm <- chmNew("Demo reduced dimension coordinates", mat)
    hm <- chmAddReducedDim(hm, "column", prc, "PCA", 3, "PC")
    umc <- umap::umap(t(mat), n_neighbors = 8)
    hm <- chmAddReducedDim(hm, "column", umc, "UMAP")
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  prc <- prcomp(matrix)
  hm <- chmNew("Demo reduced dimension coordinates", matrix)
  hm <- chmAddReducedDim(hm, "column", prc, "PCA", 3, "PC")
  umc <- umap::umap(t(matrix), n_neighbors = 8)
  hm <- chmAddReducedDim(hm, "column", umc, "UMAP")

## End(Not run)

Add a link to related information to the NGCHM.

Description

Add a link to related information to the NGCHM.

Usage

chmAddRelated(chm, group, link, description)

## S4 method for signature 'ngchm,character,character,character'
chmAddRelated(chm, group, link, description)

Arguments

Value

The extended chm.

Add a group of related links to the NGCHM.

Description

Add a group of related links to the NGCHM.

Usage

chmAddRelatedGroup(chm, name, header, linktype, blurb)

## S4 method for signature 'ngchm,character,character,character,character'
chmAddRelatedGroup(chm, name, header, linktype, blurb)

## S4 method for signature 'ngchm,character,character,character,missing'
chmAddRelatedGroup(chm, name, header, linktype)

Arguments

Value

The extended chm.

Add a CHM-specific axis type function to a NGCHM.

Description

Adds a CHM-specific axis type function to a Next Generation Clustered Heat Map (NGCHM) and returns the extended CHM. Multiple axis type functions may be added to either axis. When the NGCHM is made, any specific Axis functions matching the specified axis type will be automatically added to the appropriate axis menu.

Usage

chmAddSpecificAxisTypeFunction(chm, where, type, label, func)

## S4 method for signature 'ngchm,character,character,character,ngchmJS'
chmAddSpecificAxisTypeFunction(chm, where, type, label, func)

## S4 method for signature 'ngchm,character,character,character,character'
chmAddSpecificAxisTypeFunction(chm, where, type, label, func)

Arguments

Value

The extended chm.

See Also

chmListTypes()

ngchmAxisType

Add TSNE coordinates to an NG-CHM.

Description

Add TSNE coordinates as hidden covariate bars to an axis of an NG-CHM. One hidden covariate bar is added for each TSNE coordinate. Coordinates have names 'BASENAME.coordinate.N', where BASENAME is specified by the parameter basename (default TSNE) and N ranges from 1 to the number of added covariate bars.

Usage

chmAddTSNE(hm, axis, tsne, pointIds, basename = "TSNE")

Arguments

Details

pointIds is required because Rtsne::Rtsne() does not preserve the rownames of the data matrix it was applied to. Their values must match those on that axis of the NGCHM, but their order must match those in the data matrix passed to Rtsne::Rtsne().

Value

The NGCHM with added coordinates.

See Also

chmAddPCA()

chmAddUMAP()

chmAddUWOT()

chmAddReducedDim()

Examples

# Examples using  `chmNew()` require git to be installed.
## Not run: 
  # If the NGCHMDemoData package is installed, use it to demo usage
  if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
    data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
    mat <- TCGA.GBM.EXPR[1:10, 1:10]
    rtc <- Rtsne::Rtsne(t(mat), check_duplicates = FALSE, perplexity = 3)
    hm <- chmNew("gbm", mat)
    hm <- chmAddTSNE(hm, "column", rtc, colnames(mat))
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  rtc <- Rtsne::Rtsne(t(matrix), check_duplicates = FALSE, perplexity = 3)
  hm <- chmNew("Demo TSNE", matrix)
  hm <- chmAddTSNE(hm, "column", rtc, colnames(matrix))

## End(Not run)

Add tags to a NGCHM.

Description

Add one or more tags to a Next Generation Clustered Heat Map (NGCHM) and return the extended CHM.

Usage

chmAddTag(chm, tag)

## S4 method for signature 'ngchm,character'
chmAddTag(chm, tag)

Arguments

Value

The extended chm.

Add a file template to the NGCHM.

Description

Add a file template to the NGCHM.

Usage

chmAddTemplate(chm, source.path, dest.path, substitutions)

## S4 method for signature 'ngchm,charOrFunction,character,optList'
chmAddTemplate(chm, source.path, dest.path, substitutions)

Arguments

Value

The extended chm.

Add standard toolbox to an NG-CHM axis

Description

This function adds a toolbox to a NG-CHM (Next-Generation Clustered Heat Map) axis.

Usage

chmAddToolboxR(CHM, axis, axistype, datasetname, idstr)

## S4 method for signature 'ngchm,character,character,character,character'
chmAddToolboxR(CHM, axis, axistype, datasetname, idstr)

Arguments

Value

An updated 'ngchm' object with the new toolbox added.

Add Toolbox R2 to NG-CHM

Description

This function adds a toolbox of type R2 to a NG-CHM (Next-Generation Clustered Heat Map) object.

Usage

chmAddToolboxR2(CHM, axistype, datasetname, idstr)

## S4 method for signature 'ngchm,character,character,character'
chmAddToolboxR2(CHM, axistype, datasetname, idstr)

Arguments

Value

An updated 'ngchm' object with the new toolbox of type R2 added.

Add Toolbox RC to NG-CHM

Description

This function adds a toolbox of type RC to a NG-CHM (Next-Generation Clustered Heat Map) object.

Usage

chmAddToolboxRC(CHM, rowtype, coltype, datasetname, idstr)

## S4 method for signature 'ngchm,character,character,character,character'
chmAddToolboxRC(CHM, rowtype, coltype, datasetname, idstr)

Arguments

Value

An updated 'ngchm' object with the new toolbox of type RC added.

Add UMAP coordinates to an NG-CHM.

Description

Add UMAP coordinates as hidden covariate bars to an axis of an NG-CHM. One hidden covariate bar is added for each UMAP coordinate. Coordinates have names 'BASENAME.coordinate.N', where BASENAME is specified by the parameter basename (default UMAP) and N ranges from 1 to the number of added covariate bars.

Usage

chmAddUMAP(hm, axis, umap, basename = "UMAP")

Arguments

Value

The NGCHM with added coordinates.

See Also

chmAddPCA()

chmAddTSNE()

chmAddUWOT()

chmAddReducedDim()

Examples

# Examples using `chmNew()` require git to be installed.
## Not run: 
  # If the NGCHMDemoData package is installed, use it to demo usage
  if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
    data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
    mat <- TCGA.GBM.EXPR[1:50, 1:50]
    umc <- umap::umap(t(mat))
    hm <- chmNew("gbm", mat)
    hm <- chmAddUMAP(hm, "column", umc)
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  umc <- umap::umap(t(matrix), n_neighbors = 8)
  hm <- chmNew("Demo UMAP", matrix)
  hm <- chmAddUMAP(hm, "column", umc)

## End(Not run)

Add UWOT::UMAP coordinates to an NG-CHM.

Description

Add UWOT::UMAP coordinates as hidden covariate bars to an axis of an NG-CHM. One hidden covariate bar is added for each UMAP coordinate. Coordinates have names 'BASENAME.coordinate.N', where BASENAME is specified by the parameter basename (default UMAP) and N ranges from 1 to the number of added covariate bars.

Usage

chmAddUWOT(hm, axis, uwot, pointIds, basename = "UMAP")

Arguments

Details

pointIds is required because uwot::umap() does not preserve the rownames of the data matrix it was applied to. Their values must match those on that axis of the NGCHM, but their order must match those in the data matrix passed to uwot::umap().

Value

The NGCHM with added coordinates.

See Also

chmAddPCA()

chmAddTSNE()

chmAddUMAP()

chmAddReducedDim()

Examples

# Examples using `chmNew()` require git to be installed.
## Not run: 
  # If the NGCHMDemoData package is installed, use it to demo usage
  if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
    data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
    umc <- uwot::umap(t(TCGA.GBM.EXPR[1:50, 1:50]))
    hm <- chmNew("gbm", TCGA.GBM.EXPR[1:50, 1:50])
    hm <- chmAddUWOT(hm, "column", umc, colnames(TCGA.GBM.EXPR[1:50, 1:50]))
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  umc <- uwot::umap(t(matrix), n_neighbors = 8)
  hm <- chmNew("Demo UMAP", matrix)
  hm <- chmAddUWOT(hm, "column", umc, colnames(matrix))

## End(Not run)

Create a new Axis for adding to an NG-CHM.

Description

This function creates a new Axis for adding to a Next Generation Clustered Heat Map. You can specify any axis name here, but chmAdd only accepts row, column, and both.

Usage

chmAxis(axis, ...)

Arguments

Value

An object of class 'ngchmAxis' representing the newly created axis.

See Also

chmAdd()

Examples

x_axis <- chmAxis('row')
y_axis <- chmAxis('col')

Create a new AxisType for adding to an ngchmAxis.

Description

This function creates a new AxisType for adding to an ngchmAxis.

Usage

chmAxisType(typename, func)

Arguments

Value

An object of class 'ngchmAxisType' representing the newly created axis type.

See Also

chmAxis()

Bind values to an existing JS function.

Description

Create a new JS function by binding values to extra parameters of an existing JS function.

Usage

chmBindFunction(name, fn, bindings)

## S4 method for signature 'character,ngchmJS,list'
chmBindFunction(name, fn, bindings)

## S4 method for signature 'character,character,list'
chmBindFunction(name, fn, bindings)

Arguments

Value

A new 'ngchmJS' object representing the bound function.

See Also

chmNewFunction()

Browse the NGCHMs on the specified server in the viewer.

Description

Opens the NG-CHM browser page in the viewer.

Usage

chmBrowse(server = NULL, viewer = NULL)

Arguments

Value

None. This function is used for its side effects of opening a web browser to view the NG-CHM server.

See Also

utils::browseURL()

Set the column order of data shown in a NGCHM.

Description

This function sets the column order for a NG-CHM (Next-Generation Clustered Heat Map) object.

Usage

chmColOrder(chm) <- value

## S4 replacement method for signature 'ngchm,optDendrogram'
chmColOrder(chm) <- value

Arguments

Value

An updated 'ngchm' object with the new column order.

See Also

"chmRowOrder<-"

Get the color map of an NG-CHM object.

Description

Get the color map of an NG-CHM object.

Usage

chmColorMap(x)

Arguments

Value

An ngchmColormap

See Also

chmNewColorMap

Examples

# If the NGCHMDemoData package is installed, use it to demo usage
if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
  data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
  colormap <- chmColorMap(chmNewDataLayer("New layer", TCGA.GBM.EXPR[1:3, 1:3]))
}
matrix <- matrix(rnorm(100),
  nrow = 10, ncol = 10,
  dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
)
colormap <- chmColorMap(chmNewDataLayer("New layer", matrix))

Set the color map of an NG-CHM object

Description

Set the color map of an NG-CHM object

Usage

chmColorMap(x) <- value

Arguments

Value

The modified NG-CHM object.

See Also

chmColorMap

Examples

# If the NGCHMDemoData package is installed, use it to demo usage
if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
  data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
  dataLayer <- chmNewDataLayer("GBM layer", TCGA.GBM.EXPR[1:30, 1:30])
  chmColorMap(dataLayer) <- chmNewColorMap(c(2, 14))
}
# Small example not requiring NGCHMDemoData
matrix <- matrix(rnorm(100),
  nrow = 10, ncol = 10,
  dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
)
dataLayer <- chmNewDataLayer("my layer", matrix)
chmColorMap(dataLayer) <- chmNewColorMap(c(2, 14))

Get the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCovariate.

Description

Get the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCovariate.

Usage

chmColors(x)

Arguments

Value

A character string vector of the map colors.

See Also

ngchm

Examples

# If the NGCHMDemoData package is installed, use it to demo usage
if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
  data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
  colors <- chmColors(chmNewDataLayer("GBM Expression", TCGA.GBM.EXPR[1:50, 1:50]))
}
# Small example not requiring NGCHMDemoData
matrix <- matrix(rnorm(100),
  nrow = 10, ncol = 10,
  dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
)
colors <- chmColors(chmNewDataLayer("my layer", matrix))

Set the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCovariate.

Description

Set the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCovariate.

Usage

chmColors(x) <- value

Arguments

Value

The modified NG-CHM object.

See Also

chmColors

Examples

# If the NGCHMDemoData package is installed, use it to demo usage
if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
  data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
  layer <- chmNewDataLayer("GBM Layer", TCGA.GBM.EXPR[1:50, 1:50])
  chmColors(layer) <- c("blue", "white", "red")
}
# Small example not requiring NGCHMDemoData
matrix <- matrix(rnorm(100),
  nrow = 10, ncol = 10,
  dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
)
layer <- chmNewDataLayer("my layer", matrix)
chmColors(layer) <- c("blue", "white", "red")

Get a covariate attached to an NG-CHM dataset.

Description

Get a covariate attached to an NG-CHM dataset.

Usage

chmCovariate(dataset, fullname, where)

Arguments

Value

A ngchmCovariate or NULL.

See Also

ngchmCovariate

chmNewCovariate

chmCovariateBar

Examples

# If the NGCHMDemoData package is installed, use it to create demo usage
if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
  data(TCGA.GBM.Demo, package = "NGCHMDemoData")
  dataset <- chmNewDataset("gbmexpr", "TCGA GBM Expression Data", TCGA.GBM.ExpressionData)
  dataset <- chmAddCovariate(
    dataset, "column",
    chmNewCovariate("TP53 Mutation", TCGA.GBM.TP53MutationData)
  )
  tp53_mutation <- chmCovariate(dataset, "TP53 Mutation")
}
# Small example not requiring NGCHMDemoData
matrix <- matrix(rnorm(100),
  nrow = 10, ncol = 10,
  dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
)
dataset <- chmNewDataset("Demo", "Random Demo Dataset", matrix)
covariate <- setNames(rnorm(10), colnames(matrix))
dataset <- chmAddCovariate(dataset, "column", chmNewCovariate("Random Covariate", covariate))
random_covariate <- chmCovariate(dataset, "Random Covariate")

Get a covariate bar attached to an NG-CHM.

Description

Get a covariate bar attached to an NG-CHM.

Usage

chmCovariateBar(hm, fullname, where)

Arguments

Value

An ngchmBar or NULL.

See Also

ngchmBar

chmNewCovariateBar

chmCovariate

Examples

# Examples using `chmNew()` require git to be installed and available.
## Not run: 
  # If the NGCHMDemoData package is installed, use it to demo usage
  if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
    # Create example NGCHM with covariate bar
    data(TCGA.GBM.Demo, package = "NGCHMDemoData")
    hm <- chmNew("gbmexpr", TCGA.GBM.ExpressionData[1:50, 1:50])
    hm <- chmAddCovariateBar(
      hm, "column",
      chmNewCovariate("TP53 Mutation", TCGA.GBM.TP53MutationData[1:50])
    )
    # Get covariate bar by name
    tp53_covariate_bar <- chmCovariateBar(hm, "TP53 Mutation")
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  hm <- chmNew("Demo", matrix)
  covariate <- setNames(rnorm(10), colnames(matrix))
  hm <- chmAddCovariateBar(hm, "column", chmNewCovariate("my covariate", covariate))
  my_covariate_bar <- chmCovariateBar(hm, "my covariate")

## End(Not run)

Create a new NG-CHM Collection

Description

This function creates a new NG-CHM (Next-Generation Clustered Heat Map) collection on the server.

Usage

chmCreateCollection(path, recursive = FALSE)

Arguments

Details

The path is a sequence of components separated by slashes (/). If the path begins with a double slash (//) the following component is interpreted as a server name. If the server name is omitted (i.e. empty) the default server will be used. If the path does not begin with a double slash, the current server will be used.

If the path begins with a slash, the components (following the server, if specified) are interpreted relative to the root collection of the server concerned. Otherwise, they are interpreted relative to the current collection.

The interpretation of each path component is server specific.

Value

None. This function is used for its side effects of creating a new collection on the server.

See Also

chmCurrentCollection()

Create an ngchmServer object for a managed NG-CHM server

Description

Create an ngchmServer object called 'serverName' (see details). The new ngchmServer object is returned and registered so that it can be referenced by name, including retrieval using chmServer. This library will communicate with the NG-CHM using the private address. Returned URLs for viewing NG-CHMs will use the public address.

Usage

chmCreateManagedServer(
  serverName,
  privateAddr,
  publicAddr = NULL,
  chmPort = 80,
  managerPort = 18080,
  serviceName = "default",
  ...
)

Arguments

Value

The created (and registered) ngchmServer object.

See Also

chmServer()

chmCreateServer()

Create an ngchmServer object from a specification.

Description

Create an ngchmServer object called 'serverName' from the specification 'serverSpec' (see details). serverOptions override those in the specification files option by option. The new ngchmServer object is returned and registered so that it can be referenced by name, including retrieval using chmServer.

Usage

chmCreateServer(serverName, serverSpec = NULL, serverOptions = NULL)

Arguments

Details

serverSpec can be any of:

A configuration directory path.

The specification will be read from a file 'config.txt' in that directory.

An NGCHM server URL (ending in '/chm' or '/Viewer' for instance).

A minimal specification will be inferred. Known methods for uploading NGCHMs to the server will be autoprobed unless specified manually.

A URL referencing a configuration file (must end in '/config.txt').

The specification will be read from the specified URL.

serverOptions can include both protocol-specific options and the following generic options:

'serverURL'.

The URL for the NGCHM server.

'serverProtocol'.

The protocol to be used for uploading etc. NGCHMs to the server.

'jarFile'.

The jarFile used to build NGCHMs.

'traceLevel'.

The amount of trace to output. Defaults to "PROGRESS".

Value

The created (and registered) ngchmServer object.

See Also

chmServer()

ngchmServer

ngchmGetServerProtocol()

ngchmServerProtocol

Get the user's current collection

Description

Get the user's current collection

Usage

chmCurrentCollection()

Value

the identity of the current collection

See Also

chmSetCollection()

Get the user's current server

Description

Get the user's current server

Usage

chmCurrentServer()

Value

the identity of the current server

See Also

chmListServers()

chmServer()

chmSetCollection()

Return default column order of an NGCHM

Description

Return default column order of an NGCHM

Usage

chmDefaultColOrder(chm)

Arguments

Value

Shaid of a dendrogram suitable for use as the chm's column order.

Return default row order of an NGCHM

Description

Return default row order of an NGCHM

Usage

chmDefaultRowOrder(chm)

Arguments

Value

Shaid of a dendrogram suitable for use as the chm's row order.

Get the name of a NGCHM server.

Description

Return the name of a Next Generation Clustered Heat Map (NGCHM) server.

Usage

chmDeployServer(server)

## S4 method for signature 'ngchmServer'
chmDeployServer(server)

Arguments

Value

The name of the server.

See Also

ngchmServer

Export a standalone NGCHM to a file.

Description

Create a standalone viewer for the NGCHM in the specified file. This function requires Java 11 and the NGCHMSupportFiles package.

Usage

chmExportToFile(
  chm,
  filename,
  overwrite = FALSE,
  shaidyMapGen,
  shaidyMapGenJava,
  shaidyMapGenArgs
)

Arguments

Details

The NGCHMSupportFiles package can be installed from the R-universe repository:

install.packages('NGCHMDemoData',
repos = c('https://md-anderson-bioinformatics.r-universe.dev',
'https://cloud.r-project.org'))

Value

the rendered NGCHM

Export a standalone HTML containing the NGCHM to a file.

Description

Create a standalone HTML containing the NGCHM in the specified file. This function requires Java 11 and the NGCHMSupportFiles package.

Usage

chmExportToHTML(
  chm,
  filename,
  overwrite = FALSE,
  shaidyMapGen,
  shaidyMapGenJava,
  shaidyMapGenArgs,
  ngchmWidgetPath
)

Arguments

Details

The NGCHMSupportFiles package can be installed from the R-universe repository:

install.packages('NGCHMDemoData',
repos = c('https://md-anderson-bioinformatics.r-universe.dev',
'https://cloud.r-project.org'))

Value

filename

Export a PDF of the NGCHM to a file.

Description

Create a PDF of the NGCHM in the specified file. This function requires Java 11 and the NGCHMSupportFiles package.

Usage

chmExportToPDF(
  chm,
  filename,
  overwrite = FALSE,
  shaidyMapGen,
  shaidyMapGenJava,
  shaidyMapGenArgs
)

Arguments

Details

The NGCHMSupportFiles package can be installed from the R-universe repository:

install.packages('NGCHMDemoData',
repos = c('https://md-anderson-bioinformatics.r-universe.dev',
'https://cloud.r-project.org'))

Value

filename

Get Javascript function name for accessing a specific string field in each element of string vector.

Description

This function returns the name of a Javascript function thats accepts a string vector as its parameter, and for each string in the vector splits the string into fields separated by fieldsep, and accesses field idx (zero origin). The function returns a vector of these fields.

Usage

chmFieldAccessFunction(fieldsep, idx)

Arguments

Details

The name of the function returned for a specific fieldsep and idx will be constant within an R session, but may differ between R sessions (or if this library is unloaded and reloaded).

Value

The name of the newly created field access function.

See Also

chmGetFunction()

chmStringopFunction()

Examples

# Create a new field access function that splits the input string at ',' and
# returns the first field.
chmFieldAccessFunction(',', 1)
# Create a new field access function that splits the input string at '-' and
# returns the second field.
chmFieldAccessFunction('-', 2)

Get the dataset from an NG-CHM object

Description

This function retrieves the dataset associated with a specific NG-CHM (Next-Generation Clustered Heat Map).

Usage

chmGetDataset(object)

## S4 method for signature 'ngchmLayer'
chmGetDataset(object)

Arguments

Value

The dataset associated with the specified object.

Get per-user configuration for a specific deploy Server.

Description

This function retrieves the configuration of a specified NG-CHM (Next-Generation Clustered Heat Map) deployment server.

Usage

chmGetDeployServerConfig(server)

Arguments

Value

The configuration of the specified server if it exists, otherwise NULL.

Get a predefined Javascript function for use in NGCHM menus

Description

This function returns a predefined Javascript function that can be used when building a Next Generation Clustered Heat Map.

Usage

chmGetFunction(name)

Arguments

Value

An object of class ngchmFunction if found, NULL otherwise.

See Also

chmAddMenuItem()

chmNewFunction()

ngchmAxisFunction

ngchmMatrixFunction

Get the file path to the specified overview file.

Description

This function returns the file path to the specified overview image of the CHM. The CHM must be made before the file can be accessed. If idx is specified, format if given must equal that of the overview image, and the path to that overview image is returned. If idx is not specified, the file path to the first overview of the given format (default 'png') is returned.

Usage

chmGetOverview(chm, format = NULL, idx = NULL)

Arguments

Value

The path to the retrieved overview.

Get Property from NG-CHM

Description

This function retrieves a specific property from a NG-CHM (Next-Generation Clustered Heat Map) object.

Usage

chmGetProperty(object, label)

## S4 method for signature 'ngchmVersion2,character'
chmGetProperty(object, label)

Arguments

Value

The property associated with the specified label in the 'ngchmVersion2' object.

Get information about a type name.

Description

This function gets any registered information about a type name used for determining row and column linkouts. Registration of a typename is (currently) not required in order to use it, so it's possible for valid type name not to have any registered information.

Usage

chmGetTypeInfo(typename)

Arguments

Value

Object of class "ngchm.type.info" containing basic information about the type.

See Also

chmListTypes()

chmRegisterType()

Get the URL for an installed NGCHM.

Description

Return the URL for accessing the specified Next Generation Clustered Heat Map (NGCHM) on the specified server.

Usage

chmGetURL(chm, ...)

## S4 method for signature 'character'
chmGetURL(chm, server = NULL, ...)

## S4 method for signature 'ngchm'
chmGetURL(chm, server = NULL, ...)

Arguments

Value

A character string representing the URL of the specified NG-CHM on the specified server.

See Also

ngchmServer

ngchm

Determine if the NG-CHM has the given property.

Description

This function checks if a specific property exists in a NG-CHM (Next-Generation Clustered Heat Map) object.

Usage

chmHasProperty(object, label)

## S4 method for signature 'ngchmVersion2,character'
chmHasProperty(object, label)

Arguments

Value

A logical value indicating whether the specified property(ies) exist in the 'ngchmVersion2' object. If 'label' is a vector, a logical vector is returned.

Add an NG-CHM to an NG-CHM collection.

Description

Add the given Next-Generation Clustered Heat Map (NG-CHM) to the specified collection (default: current collection).

Usage

chmInstall(chm, ...)

## S4 method for signature 'ngchm'
chmInstall(chm, path, ...)

Arguments

Value

The installed chm.

See Also

ngchmServer

ngchm

chmUninstall()

chmMakePrivate()

chmMakePublic()

Get the label/name of an NG-CHM object.

Description

Get the label/name of an NG-CHM object.

Usage

chmLabel(x)

Arguments

Value

A character string (or a vector of strings for an ngchmColormap)

See Also

ngchm

Examples

chmLabel(chmNew("New CHM"))

Set the label/name of an NG-CHM object

Description

Set the label/name of an NG-CHM object

Usage

chmLabel(x) <- value

Arguments

Value

The modified NG-CHM object.

See Also

chmLabel

Examples

hm <- chmNew("Old name")
chmLabel(hm) <- "A new name"

Get a specified Data Layer from an NG-CHM.

Description

This function returns a Data Layer contained in a Next Generation Clustered Heat Map.

Usage

chmLayer(hm, label)

Arguments

Value

An object of class ngchmLayer or NULL.

See Also

ngchmLayer

Examples

# Examples using `chmNew()` require git to be installed and available.
## Not run: 
 # If the NGCHMDemoData package is installed, use it to create an example usage
 if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
    # Create example NGCHM
    data(TCGA.GBM.Demo, package = "NGCHMDemoData")
    matrix <- TCGA.GBM.ExpressionData[1:50, 1:50]
    hm <- chmNew("New Heat Map") + chmNewDataLayer("my layer", matrix)
    layer <- chmLayer(hm, "my layer")
    same_layer <- chmLayer(hm, 1)
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  hm <- chmNew("New Heat Map") + chmNewDataLayer("my layer", matrix)
  layer <- chmLayer(hm, "my layer")
  same_layer <- chmLayer(hm, 1)

## End(Not run)

Set (or append) a specified Data Layer in an NG-CHM.

Description

This function sets a Data Layer in a Next Generation Clustered Heat Map.

Arguments

Value

An object of class ngchm.

See Also

ngchmLayer

chmNewDataLayer

Examples

# If the NGCHMDemoData package is installed, use demo usage
if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
  data(TCGA.GBM.Demo, package = "NGCHMDemoData")
  matrix <- TCGA.GBM.ExpressionData[1:50, 1:50]
  hm <- chmNew("New Heat Map")
  chmLayer(hm, "Layer 1") <- matrix
  chmLayer(hm, 1, cuts_color = "#fefefe") <- chmNewDataLayer("New data layer", matrix + 1)
}
# Small example not requiring NGCHMDemoData
matrix <- matrix(rnorm(100),
  nrow = 10, ncol = 10,
  dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
)
hm <- chmNew("New Heat Map")
chmLayer(hm, "Layer 1") <- matrix
chmLayer(hm, 1, cuts_color = "#fefefe") <- chmNewDataLayer("New data layer", matrix + 1)

List the predefined Javascript functions available for use in NGCHM menus.

Description

This function lists the predefined Javascript functions available for use in NGCHM menus.

Usage

chmListFunctions(re = ".*")

Arguments

Value

A string containing the names and descriptions of the matching functions.

See Also

chmAddMenuItem()

chmGetFunction()

chmRegisterFunction()

grep()

Examples

chmListFunctions() # List all functions.
chmListFunctions('^chm') # List all functions whose names start with 'chm'.

List NG-CHM Servers

Description

This function lists all NG-CHM (Next-Generation Clustered Heat Map) servers that are currently available.

Usage

chmListServers()

Value

A character vector containing the names of all available servers.

Examples

servers <- chmListServers() # Get a list of all available servers.

List known axis types.

Description

This function returns a list of the axis types for which axis- or matrix- menu entries may be defined.

Usage

chmListTypes(re = ".*")

Arguments

Value

a character vector of axis type names

See Also

chmAddAxisType()

Load CHM from NG-CHM server

Description

Load an R CHM object from an NG-CHM server. The CHM concerned must have been built using this library, version 0.9.4 or later.

Usage

chmLoadCHM(serverOrURL, name)

## S4 method for signature 'ngchmServer,character'
chmLoadCHM(serverOrURL, name)

## S4 method for signature 'character,character'
chmLoadCHM(serverOrURL, name)

## S4 method for signature 'character,missing'
chmLoadCHM(serverOrURL, name)

Arguments

Value

An object of class 'ngchm' representing the loaded NG-CHM.

Load an NG-CHM from an NG-CHM server.

Description

Load an NG-CHM from an NG-CHM server.

Usage

chmLoadShaidyCHM(mapid, debug = FALSE)

Arguments

Value

An object of class ngchm.

See Also

chmInstall()

ngchmPushSourceServer()

Compile a NGCHM.

Description

Deprecated. Users should no longer call this method directly.

Usage

chmMake(chm, ...)

## S4 method for signature 'ngchm'
chmMake(chm, ...)

Arguments

Details

Compiles the specified Next Generation Clustered Heat Map (NGCHM) in preparation for installation.

Value

The chm

See Also

ngchmServer

ngchm

chmNew()

chmInstall()

ngchmMakeFormat.original()

Make NG-CHM Private on Server

Description

This function makes a specific NG-CHM (Next-Generation Clustered Heat Map) private on a specified server.

Usage

chmMakePrivate(server, chm)

## S4 method for signature 'ngchmServer,character'
chmMakePrivate(server, chm)

## S4 method for signature 'ngchmServer,ngchm'
chmMakePrivate(server, chm)

## S4 method for signature 'character,ngchm'
chmMakePrivate(server, chm)

## S4 method for signature 'character,character'
chmMakePrivate(server, chm)

Arguments

Value

No return value. The function is called for its side effect of making the specified NG-CHM private on the specified server.

See Also

ngchmServer

ngchm

chmInstall()

chmUninstall()

chmMakePublic()

Make NG-CHM Public on Server

Description

This function makes a specific NG-CHM (Next-Generation Clustered Heat Map) public on a specified server.

Usage

chmMakePublic(server, chm)

## S4 method for signature 'ngchmServer,character'
chmMakePublic(server, chm)

## S4 method for signature 'ngchmServer,ngchm'
chmMakePublic(server, chm)

## S4 method for signature 'character,ngchm'
chmMakePublic(server, chm)

## S4 method for signature 'character,character'
chmMakePublic(server, chm)

Arguments

Value

No return value. The function is called for its side effect of making the specified NG-CHM public on the specified server.

See Also

ngchmServer

ngchm

chmInstall()

chmUninstall()

chmMakePrivate()

Open the NG-CHM Manager

Description

This function opens a web browser to view the NG-CHM (Next-Generation Clustered Heat Map) Manager on the specified server.

Usage

chmManager(server = NULL, viewer = NULL)

Arguments

Value

None. This function is used for its side effects of opening a web browser to view the NG-CHM Manager.

See Also

utils::browseURL()

Get the name of a NGCHM.

Description

This function returns the name of a Next Generation Clustered Heat Map (NGCHM) object.

Usage

chmName(chm)

## S4 method for signature 'ngchm'
chmName(chm)

Arguments

Value

A string.

See Also

ngchm

Create a new NGCHM.

Description

This function creates a Next Generation Clustered Heat Map (NGCHM) object in memory. Additional parameters will be added to the new NGCHM (see chmAdd). The bare NGCHM needs at least one data layer added to it before it can be compiled. This function requires git to be installed.

Usage

chmNew(
  name,
  ...,
  rowOrder = chmDefaultRowOrder,
  rowDist = "correlation",
  rowAgglom = "ward.D2",
  colOrder = chmDefaultColOrder,
  colDist = "correlation",
  colAgglom = "ward.D2",
  rowAxisType = NULL,
  colAxisType = NULL,
  rowCovariates = NULL,
  colCovariates = NULL,
  format = "original",
  rowGapLocations = NULL,
  rowGapWidth = 5,
  colGapLocations = NULL,
  colGapWidth = 5,
  overview = c(),
  logLevel = "INFO",
  logFile = NULL
)

Arguments

Value

An object of class ngchm

See Also

ngchm

ngchmServer

chmAdd()

chmAddAxisType()

chmAddCovariateBar()

chmAddProperty()

chmAddOverview()

chmInstall()

chmExportToFile()

chmExportToPDF()

chmExportToHTML()

Examples

mychm <- chmNew("test_chm")
mychm <- chmNew("test_chm", rowGapLocations = c(3, 5))
mychm <- chmNew("test_chm", rowGapLocations = chmTreeGaps(4))
mychm <- chmNew("test_chm", rowGapWidth = 3)

Create a new Color Map for use in constructing a NGCHM

Description

This function creates a new Color Map suitable for use in constructing Data Layers and Covariates in Next Generation Clustered Heat Maps. Color maps can be used in both discrete and continuous contents. In a discrete context, values specifies the properties of series. In a continuous context, values specifies the break points.

Usage

chmNewColorMap(
  values,
  colors = NULL,
  names = NULL,
  shapes = NULL,
  zs = NULL,
  type = "linear",
  missing.color = NULL,
  palette = NULL
)

Arguments

Details

If values is a matrix, the function will estimate a suitable sequence of color break points. For a quantile color map, the matrix data is ignored. For a linear color map, it will use equispaced values between a low value and a high value. The low value is the median of the minima of each row in the matrix, and the high value is the median of the row maxima. If the low and high values have different signs, the values will be symmetric about zero.

Value

An object of class ngchmColormap

See Also

ngchmColormap

chmNewDataLayer()

chmNewCovariateBar()

Examples

noise.colors <- chmNewColorMap(c(0, 1, 2),
  c("green", "black", "red"),
  missing.color = "yellow"
)
bar.colors <- chmNewColorMap(c("small", "big"),
  c("#00FFFF", "#FF00FF"),
  type = "quantile"
)

Create a new Covariate for adding to an NGCHM auxilary dataset.

Description

This function creates a new Covariate suitable for a covariate bar or attaching to an NGCHM auxilary dataset.

Usage

chmNewCovariate(
  fullname,
  values,
  value.properties = NULL,
  type = NULL,
  covabbv = NULL
)

Arguments

Value

An object of class ngchmCovariate.

See Also

ngchmCovariate

chmAddCovariate()

chmNewColorMap()

Create a new covariate Bar for a NGCHM

Description

This function creates a new covariate bar suitable for adding to a Next Generation Clustered Heat Map.

Usage

chmNewCovariateBar(
  covar,
  display = "visible",
  thickness = as.integer(10),
  merge,
  barType,
  loBound,
  hiBound,
  fgColor,
  bgColor
)

Arguments

Value

An object of class ngchmBar

See Also

ngchmBar

chmNewColorMap()

chmAddCovariateBar()

Examples

bar.data <- ifelse(rnorm(1000) < 0, "negative", "non-negative")
names(bar.data) <- sprintf("Sample%d", 1:length(bar.data))
bar.colors <- chmNewColorMap(c("negative", "non-negative"),
  c("white", "black"),
  missing.color = "red"
)
covar <- chmNewCovariate("Group", bar.data, bar.colors, "discrete")
bar <- chmNewCovariateBar(covar)

Create a new Data Layer for a NGCHM.

Description

This function creates a new Data Layer suitable for adding to a Next Generation Clustered Heat Map.

Usage

chmNewDataLayer(label, data, colors, summarizationMethod, cuts_color)

Arguments

Value

An object of class ngchmLayer

See Also

ngchmLayer

chmNewColorMap()

chmAddLayer()

Examples

noise <- matrix(runif(1000) + runif(1000 * 1000), nrow = 1000)
rownames(noise) <- sprintf("Row%d", 1:nrow(noise))
colnames(noise) <- sprintf("Col%d", 1:ncol(noise))
noise.colors <- chmNewColorMap(c(0, 1, 2),
  c("green", "black", "red"),
  missing.color = "yellow"
)
layer <- chmNewDataLayer("Noisy Data", noise, noise.colors)

Create a new Dataset for a NGCHM.

Description

This function creates a new Dataset suitable for attaching to a Next Generation Clustered Heat Map.

Usage

chmNewDataset(
  name,
  description,
  data,
  row.type = NULL,
  column.type = NULL,
  row.covariates = NULL,
  column.covariates = NULL
)

Arguments

Value

An object of class ngchmDataset

See Also

ngchmDataset

ngchmCovariate

chmAddDataset()

Create a new Dialog for a NGCHM.

Description

This function creates a new Dialog suitable for adding to a Next Generation Clustered Heat Map.

Usage

chmNewDialog(id, title, fn)

Arguments

Value

An object of class ngchmDialog

See Also

chmAdd()

chmAddDialog()

Create a new Javascript function for adding to a NGCHM menu.

Description

This function creates a new Javascript function object for adding to a Next Generation Clustered Heat Map menu.

Usage

chmNewFunction(
  name,
  description,
  implementation,
  extraParams = NULL,
  requires = NULL,
  global = FALSE
)

Arguments

Value

An object of class ngchmJS

See Also

ngchmJS

chmAddMenuItem()

chmBindFunction()

chmRegisterFunction()

Examples

alertFn <- chmNewFunction("showAlert", "Display the parameter in an alert box",
  "function showAlert(label) { alert(label); }",
  global = TRUE
)
dbLookup <- chmNewFunction(
  "dbLookup", "Lookup the parameter in a database",
  "function showAlert(database, label) { alert(database[label]); }",
  c("database")
)

Create a new Property for adding to a NGCHM.

Description

This function creates a new Property object for adding to a Next Generation Clustered Heat Map.

Usage

chmNewProperty(label, value)

Arguments

Value

An object of class ngchmProperty

See Also

ngchm

chmAddProperty()

Examples

prop <- chmNewProperty(
  "chm.info.caption",
  "This is a nifty new CHM."
)

Create a new object representing a NGCHM server.

Description

This function creates a new object that represents a NGCHM server.

Usage

chmNewServer(
  serverName,
  serverPort = 8080,
  deployServer = NULL,
  protoOpts = NULL,
  jarFile = NULL,
  serverURL = NULL
)

Arguments

Value

An object of class ngchmServer

See Also

ngchmServer

chmInstall()

chmUninstall()

Examples

cloudServ <- chmNewServer("dnsname.domain")

Return original column order of an NGCHM

Description

Return original column order of an NGCHM

Usage

chmOriginalColOrder(chm)

Arguments

Value

Shaid of a label order suitable for use as the chm's column order.

Return original row order of an NGCHM

Description

Return original row order of an NGCHM

Usage

chmOriginalRowOrder(chm)

Arguments

Value

Shaid of a label order suitable for use as the chm's row order.

Create NG-CHM Properties

Description

This function creates one or more NG-CHM (Next-Generation Clustered Heat Map) properties.

Usage

chmProperties(...)

Arguments

Value

A list of properties. Each property is represented as a list with two elements: 'label' and 'value'.

See Also

chmAdd()

Examples

# Create three properties: 'prop1', 'prop2', and 'prop3'.
props <- chmProperties(prop1 = "value1", prop2 = 2, prop3 = TRUE)

Get the value of an NG-CHM property.

Description

Get the value of an NG-CHM property.

Usage

chmProperty(hm, label)

Arguments

   Well-known property labels used by the NG-CHM system include:

   * "chm.info.caption"  A paragraph describing the NG-CHM's contents (set by user).
  * "chm.info.built.time"  The date and time the NG-CHM was saved (set by system).

Value

A property value or NULL.

See Also

ngchm

Examples

hm <- chmNew("Empty")
chmProperty(hm, "chm.info.caption")

Set the value of an NG-CHM property.

Description

Set the value of an NG-CHM property.

Usage

chmProperty(x, label) <- value

Arguments

Value

The modified NG-CHM object.

See Also

ngchm

Examples

hm <- chmNew("Empty")
chmProperty(hm, "chm.info.caption") <- "Nothing to see here"

Return random column order of an NGCHM

Description

Return random column order of an NGCHM

Usage

chmRandomColOrder(chm)

Arguments

Value

Shaid of a label order suitable for use as the chm's column order.

Return random row order of an NGCHM

Description

Return random row order of an NGCHM

Usage

chmRandomRowOrder(chm)

Arguments

Value

Shaid of a label order suitable for use as the chm's row order.

Register a predefined Javascript function for use in NGCHM Axis menus.

Description

This function registers a Javascript function that will be automatically added to the appropriate axis menu(s) when building a Next Generation Clustered Heat Map for axes that match the function's axis type. This function is intended for use by NGCHM system developers.

Usage

chmRegisterAxisFunction(type, label, fn)

Arguments

Value

None. This function is used for its side effects of registering a new axis function.

See Also

chmAddAxisType()

chmRegisterMatrixFunction()

chmRegisterTypeMapper()

chmNewFunction()

Register a predefined Javascript function for use in NGCHM menus.

Description

This function registers a Javascript function that can be used when building a Next Generation Clustered Heat Map. This function is intended for use by NGCHM system developers.

Usage

chmRegisterFunction(fn)

Arguments

Value

The registered function.

See Also

chmAddMenuItem()

chmNewFunction()

ngchmAxisFunction

ngchmMatrixFunction

Define and register a Javascript function for obtaining a specific metadata value.

Description

This function defines and registers a Javascript function for obtaining a specific metadata value and returning it as a javascript list. The function is suitable for use as an axis type accessor function.

Usage

chmRegisterGetMetadataFunction(functionName, metadataColumnName)

Arguments

Value

The registered function.

See Also

chmAddAxisType()

chmGetFunction()

chmListFunctions()

Register a predefined Javascript function for use in NGCHM Matrix menus.

Description

This function registers a Javascript function that will be automatically added to the matrix menu when building a Next Generation Clustered Heat Map for matrices whose rows and columns match then function's axes types. This function is intended for use by NGCHM system developers.

Usage

chmRegisterMatrixFunction(rowtype, columntype, label, fn)

Arguments

Value

None. This function is used for its side effects of registering a new function in the NGCHM matrix menues.

See Also

chmAddAxisType()

chmRegisterAxisFunction()

chmRegisterTypeMapper()

chmNewFunction()

Register a Javascript function for use in the NGCHM toolbox.

Description

This function registers a Javascript function that can included in the toolbox of an NGCHM. This function is intended for use by NGCHM system developers.

Usage

chmRegisterToolboxFunction(tbtype, menulabel, jsfn)

Arguments

Value

None. This function is used for its side effects of registering a new toolbox function.

See Also

chmNewFunction()

ngchmAxisFunction

ngchmMatrixFunction

Register a type name.

Description

This function registers a type name used for determining row and column linkouts. This function is intended to be used by NGCHM system developers to record basic information about the semantic interpretation of a type name. Registration of a typename is (currently) not required in order to use it.

Usage

chmRegisterType(typename, description)

Arguments

Value

None. This function is used for its side effects of registering a new type.

See Also

chmListTypes()

chmGetTypeInfo()

chmRegisterTypeMapper()

Register a predefined Javascript function for converting values from one type to another.

Description

This function registers a Javascript function that will be automatically added to a Next Generation Clustered Heat Map as required for converting values from one type into another more basic type. This function is intended for use by NGCHM system developers.

Usage

chmRegisterTypeMapper(fromtype, totype, op, ...)

Arguments

Value

NULL

op can have the following values:

• 'field' Split source into fields separated by 'separator' and select field 'num' (0 origin)

• 'expr' Compute string expression 'expr'. 'return' value is a vector or a scalar (default)

• 'javascript' Evaluate javascript function 'fn' (deprecated)

See Also

chmAddAxisType()

chmRegisterAxisFunction()

chmRegisterMatrixFunction()

chmNewFunction()

Define and register a Javascript function for converting a lists of type values into single values.

Description

This function defines and registers a Javascript function for converting a list of type values separated by the specified separator into the single values, and registers it as a type mapper.

Usage

chmRegisterTypeSplitter(functionName, listtype, itemtype, separator)

Arguments

Value

None. This function is used for its side effects of registering a new type splitter.

See Also

chmGetFunction()

chmListFunctions()

chmRegisterTypeMapper()

Set the row order of data shown in a NGCHM.

Description

This function sets the row order for a NG-CHM (Next-Generation Clustered Heat Map) object.

Usage

chmRowOrder(chm) <- value

## S4 replacement method for signature 'ngchm,optDendrogram'
chmRowOrder(chm) <- value

Arguments

Value

An updated 'ngchm' object with the new row order.

See Also

"chmColOrder<-"

Get a registered ngchmServer object for use in making and installing NGCHMs

Description

This function returns a ngchmServer object that can be used when making and installing a Next Generation Clustered Heat Map.

Usage

chmServer(name)

Arguments

Value

An object of class ngchmServer if found, NULL otherwise. If multiple servers of the same name have been defined (in different namespaces), the most recently defined is returned.

See Also

chmInstall()

chmUninstall()

ngchmServer

Set the user's current server and/or collection

Description

The path is a sequence of components separated by slashes (/). If the path begins with a double slash (//) the following component is interpreted as a server name. If the server name is omitted (i.e. empty) the default server will be used. If the path does not begin with a double slash, the current server will be used.

Usage

chmSetCollection(path)

Arguments

Details

If the path begins with a slash, the components (following the server, if specified) are interpreted relative to the root collection of the server concerned. Otherwise, they are interpreted relative to the current collection.

The interpretation of each path component is server specific.

Value

None. This function is used for its side effects of setting the current server and collection.

See Also

chmCurrentCollection()

chmServer()

chmListServers()

Set Access Credentials for NG-CHM Server

Description

This function sets the credentials for a specific NG-CHM (Next-Generation Clustered Heat Map) server.

Usage

chmSetCredentials(resource, credentials)

## S4 method for signature 'ngchmServer,character'
chmSetCredentials(resource, credentials)

## S4 method for signature 'character,character'
chmSetCredentials(resource, credentials)

Arguments

Value

No return value. The function is called for its side effect of setting the credentials for the specified server.

Specify per-user configuration for a specific deploy Server.

Description

Specify per-user configuration for a specific deploy Server.

Usage

chmSetDeployServerConfig(server, config)

Arguments

Value

None. This function is used for its side effects of setting the deployment server configuration.

Get Javascript function name for performing a specific string operation on each element of a string vector.

Description

This function returns the name of a Javascript function thats accepts a string vector as its parameter, and for each string in the vector performs the operation stringop on the string. Stringop must be valid Javascript code that can be appended to a string value. The function returns a vector of the resulting strings.

Usage

chmStringopFunction(stringop)

Arguments

Details

The name of the function returned for a specific stringop will be constant within an R session, but may differ between R sessions (or if this library is unloaded and reloaded).

Value

A character string specifying the name of the new function.

See Also

chmGetFunction()

chmFieldAccessFunction()

Creates new treeCuts object

Description

This function was designed to facilitate setting rowGapLocations and colGapLocations in the chmNew() function. See examples section.

Usage

chmTreeGaps(numberOfCuts)

Arguments

Value

treeCuts object with specified number of tree cuts

Examples

mychm <- chmNew("test_chm", rowGapLocations = chmTreeGaps(5))

Remove an NG-CHM from Server

Description

This function removes a specific NG-CHM (Next-Generation Clustered Heat Map) from a specified server.

Usage

chmUninstall(chm, ...)

## S4 method for signature 'character'
chmUninstall(chm, server = NULL, ...)

## S4 method for signature 'ngchm'
chmUninstall(chm, ...)

Arguments

Value

No return value. The function is called for its side effect of uninstalling the specified NG-CHM from the specified server.

See Also

ngchmServer

ngchm

chmInstall()

Get the base URL for a NGCHM installed on a NGCHM server.

Description

Return the base URL of a Next Generation Clustered Heat Map (NGCHM) that has been installed on a NGCHM server.

Usage

chmUrlBase(server)

## S4 method for signature 'ngchmServer'
chmUrlBase(server)

Arguments

Value

The base URL for accessing NGCHMs installed on the server.

See Also

ngchmServer

Output Javascript code required to customize an NGCHM.

Description

This function outputs the Javascript required to customize an NGCHM.

Usage

chmWriteCustomJS(chm, filename)

Arguments

Value

None. This function is used for its side effects of writing the JavaScript to a file.

Generic method to get a dimensions matrix from obj.

Description

The return value must be NULL or a numeric matrix, each column of which is a (reduced) dimension. The rows of the returned matrix must be named.

Usage

getDimensions(obj, ...)

## Default S3 method:
getDimensions(obj, ...)

## S3 method for class 'prcomp'
getDimensions(obj, ...)

## S3 method for class 'umap'
getDimensions(obj, ...)

## S3 method for class 'Seurat'
getDimensions(obj, dimName, ...)

Arguments

Value

A matrix with one dimension per column and one named row per observation in obj.

See Also

chmAddReducedDim()

Obtain the git hash of an existing file.

Description

Obtain the git hash of an existing file.

Usage

gitHashObject(path)

Arguments

Value

a string containing the file hash

Initialize Logging

Description

This function initializes logging for the application.

Usage

initLogging(log_level, log_file = NULL)

Arguments

Value

None. This function is used for its side effects of initializing the logging.

Class representing a Next Generation Clustered Heat Map (NGCHM) under construction.

Description

An NG-CHM is produced by creating a heat map object with chmNew(), possibly modifying or augmenting it using additional functions, such as chmAddLayer(), chmAddCovariateBar(), etc., and then either saving it to a server using chmInstall() or saving it to a standalone file using chmExportToFile().

See Also

chmNew()

chmRowOrder<-()

chmColOrder<-()

chmAdd()

chmAddLayer()

chmAddCovariateBar()

chmAddDataset()

chmAddAxisType()

chmInstall()

chmExportToFile()

Add a data file to a local shaidy repository

Description

Add a data file to a local shaidy repository

Usage

ngchmAddDatasetBlob(shaidyRepo, format, filename, properties = NULL)

Arguments

Value

The file's shaid

Add a matrix reference to a collection

Description

Add a matrix reference to a collection

Usage

ngchmAddMatrixToCollection(collection, name, shaid)

Arguments

Value

An updated list contaiing details of the collection

Add an object reference to a collection

Description

Add an object reference to a collection

Usage

ngchmAddObjectToCollection(repo, uuid, shaid)

Arguments

Value

An updated list containing details of the collection

Class representing an axis of a Next Generation Clustered Heat Map (NG-CHM).

Description

Class representing an axis of a Next Generation Clustered Heat Map (NG-CHM).

See Also

chmAxis()

Class representing an axis function for Next Generation Clustered Heat Map (NGCHM).

Description

Class representing an axis function for Next Generation Clustered Heat Map (NGCHM).

Class representing a type attached to an axis in a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing a type attached to an axis in a Next Generation Clustered Heat Map (NGCHM).

Class representing a Covariate Bar on a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing a Covariate Bar on a Next Generation Clustered Heat Map (NGCHM).

Class representing custom CSS for a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing custom CSS for a Next Generation Clustered Heat Map (NGCHM).

Recursively determine if collection uuid is contained in collection A collecton always contains itself.

Description

Recursively determine if collection uuid is contained in collection A collecton always contains itself.

Usage

ngchmCollectionInCollection(collection, uuid)

Arguments

Value

TRUE iff collection contains uuid, otherwise FALSE

Create a recursive description of a collection

Description

Create a recursive description of a collection

Usage

ngchmCollectionTree(collection, depth = 0)

Arguments

Value

a string vector describing the contents of the collection

Class representing a Color Map on a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing a Color Map on a Next Generation Clustered Heat Map (NGCHM).

Class representing a Covariate attached to a Dataset

Description

Class representing a Covariate attached to a Dataset

Create and register an NGCHM server protocol implementation.

Description

This function creates and registers a protocol implementation for manipulating an NGCHM server.

Usage

ngchmCreateServerProtocol(
  protocolName,
  chmFormat,
  requiredParams,
  optionalParams,
  paramValidator,
  findCollection,
  createCollection,
  installMethod,
  uninstallMethod,
  makePrivate,
  makePublic,
  setCredentials
)

Arguments

Value

An object of class 'ngchmServerProtocol' representing the new server protocol.

Class representing a Dataset attached to a NGCHM

Description

Class representing a Dataset attached to a NGCHM

Class representing an addon dialog

Description

Class representing an addon dialog

Find a repository, if any, that contains the requested shaid

Description

Find a repository, if any, that contains the requested shaid

Usage

ngchmFindRepo(shaid, required = TRUE)

Arguments

Value

The first repository containing the shaid, otherwise NULL. The temporary repositories are searched before source repositories.

Compute shaid for a data file

Description

Compute shaid for a data file

Usage

ngchmGetDataFileShaid(format, filename)

Arguments

Value

The shaid of the data file

Get the ngchm environment (for debugging only).

Description

Get the library's internal ngchm environment to help debugging.

Usage

ngchmGetEnv()

Value

A list representing the current environment for NG-CHM.

Get a HTTR handle for the server's view/WS URL

Description

This function returns a 'handle' suitable for use with the server's view/WS URL

Usage

ngchmGetHandleHTTR(server)

Arguments

Value

An HTTR handle

Get the axis labels of a shaidy dataset or dendrogram

Description

Get the axis labels of a shaidy dataset or dendrogram

Usage

ngchmGetLabels(shaid, axis = NULL)

Arguments

Value

a list of shaids containing the labels

Get the axis labels of a shaidy dataset or dendrogram

Description

Get the axis labels of a shaidy dataset or dendrogram

Usage

ngchmGetLabelsStr(shaid, axis = NULL)

Arguments

Value

A string vector containing the axis labels of the dataset or dendrogram

Get Protocol Parameter for NG-CHM Server

Description

This function gets a protocol parameter for a specified NG-CHM (Next-Generation Clustered Heat Map) server.

Usage

ngchmGetProtoParam(server, option, default = NULL)

Arguments

Value

The value of the protocol parameter if it is found, otherwise the specified default value.

Get Server Protocol for NG-CHM

Description

This function gets a server protocol for NG-CHM (Next-Generation Clustered Heat Map) by its name.

Usage

ngchmGetServerProtocol(protocolName)

Arguments

Value

An object of class 'ngchmServerProtocol' representing the server protocol.

Initialize Shaidy Repository for NG-CHM

Description

This function initializes a Shaidy repository for NG-CHM (Next-Generation Clustered Heat Map).

Usage

ngchmInitShaidyRepository(shaidyDir)

Arguments

Value

None. This function is used for its side effects of initializing the Shaidy repository.

Class representing a custom Javascript function for a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing a custom Javascript function for a Next Generation Clustered Heat Map (NGCHM).

Class representing a Layer on a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing a Layer on a Next Generation Clustered Heat Map (NGCHM).

List defined server protocols

Description

List defined server protocols

Usage

ngchmListServerProtocols()

Value

A character vector

Load a data matrix from a local shaidy repository

Description

Load a data matrix from a local shaidy repository

Usage

ngchmLoadDatasetBlob(shaidyRepo, shaid, datatype)

Arguments

Value

a list containing details of the loaded dataset

Make an original format NGCHM.

Description

Make an original format NGCHM.

Usage

ngchmMakeFormat.original(
  chm,
  server,
  deleteOld = TRUE,
  useJAR = NULL,
  javaTraceLevel = NULL,
  javaOptions = NULL,
  buildArchive = NULL
)

Arguments

Value

The CHM

Make a shaidy format NGCHM.

Description

Make a shaidy format NGCHM.

Usage

ngchmMakeFormat.shaidy(chm)

Arguments

Value

The CHM

Class representing a matrix function for Next Generation Clustered Heat Map (NGCHM).

Description

Class representing a matrix function for Next Generation Clustered Heat Map (NGCHM).

Class representing a Menu Item for a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing a Menu Item for a Next Generation Clustered Heat Map (NGCHM).

Class representing meta data attached to an NG-CHM

Description

Class representing meta data attached to an NG-CHM

Create a new Classification Bar for a NGCHM

Description

This function is deprecated and will be removed in a future version. Please use chmNewCovariateBar. This function creates a new Classification Bar suitable for adding to a Next Generation Clustered Heat Map.

Usage

ngchmNewBar(
  label,
  type,
  data,
  colors = NULL,
  display = "visible",
  thickness = as.integer(10),
  merge,
  barType,
  loBound,
  hiBound,
  fgColor,
  bgColor
)

Arguments

Value

An object of class ngchmBar

See Also

ngchmBar

chmNewColorMap()

chmNewCovariateBar()

chmAddCovariateBar()

Create a new collection in a local shaidy repository

Description

Create a new collection in a local shaidy repository

Usage

ngchmNewCollection(shaidyRepo, labels = data.frame())

Arguments

Value

a string containing the UUID of the newly created repository

Class representing an overview of a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing an overview of a Next Generation Clustered Heat Map (NGCHM).

Class representing a Generic Property for a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing a Generic Property for a Next Generation Clustered Heat Map (NGCHM).

Check Protocol Parameters for NG-CHM

Description

Check that all required parameters are specified, and all specified parameters are either required or optional.

Usage

ngchmProtoParamCheck(params, required, optional)

Arguments

Value

None. This function is used for its side effects of checking the parameters and potentially stopping execution with an error message.

Push a local shaidy repository onto the stack of source repositories

Description

This function pushes a source repository for NG-CHM (Next-Generation Clustered Heat Map) onto the Shaidy stack.

Usage

ngchmPushSourceRepository(shaidyDir, accessMethod = "file")

Arguments

Value

None. This function is used for its side effects of pushing the source repository onto the Shaidy stack.

Push a shaidy server onto the stack of source repositories

Description

This function pushes a source server for NG-CHM (Next-Generation Clustered Heat Map) onto the Shaidy stack.

Usage

ngchmPushSourceServer(server)

Arguments

Value

None. This function is used for its side effects of pushing the source server onto the Shaidy stack.

See Also

chmLoadShaidyCHM()

chmCreateServer()

Push Temporary Repository for NG-CHM

Description

This function pushes a temporary repository for NG-CHM (Next-Generation Clustered Heat Map) onto the Shaidy stack.

Usage

ngchmPushTempRepository(shaidyDir)

Arguments

Value

None. This function is used for its side effects of pushing the temporary repository onto the Shaidy stack.

Register an ngchmServer.

Description

This function registers an ngchmServer that can be used when making and installing a Next Generation Clustered Heat Map.

Usage

ngchmRegisterServer(uuid, server)

Arguments

Value

the server that was registered

See Also

chmInstall()

chmUninstall()

ngchmUnregisterServer()

ngchmServer

Class representing a link related to a NGCHM

Description

Class representing a link related to a NGCHM

Class representing a group of related links to a NGCHM

Description

Class representing a group of related links to a NGCHM

Render a shaidy NGCHM

Description

Render a shaidy NGCHM

Usage

ngchmRenderChm(repo, shaid)

Arguments

Value

Nothing

Return response content interpreted as JSON

Description

Return response content interpreted as JSON

Usage

ngchmResponseJSON(httrResponse)

Arguments

Value

The response parsed as JSON and returned as an R object

Row center a shaidy dataset

Description

Row center a shaidy dataset

Usage

ngchmRowCenter(shaidyRepo, shaid)

Arguments

Value

A list of shaids for the row centered dataset

Save a numeric matrix as a blob in a shaidy repository

Description

Save a numeric matrix as a blob in a shaidy repository

Usage

ngchmSaveAsDatasetBlob(shaidyRepo, format, mat)

Arguments

Value

The shaid of the saved blob

Save a dendrogram as a blob in a shaidy repository

Description

Save a dendrogram as a blob in a shaidy repository

Usage

ngchmSaveAsDendrogramBlob(shaidyRepo, ddg)

Arguments

Value

The shaid of the saved blob

Save an NGCHM as a shaidy blob

Description

Save an NGCHM as a shaidy blob

Usage

ngchmSaveChmAsBlob(shaidyRepo, chm)

Arguments

Value

The shaid of the saved NGCHM

Class representing a Next Generation Clustered Heat Map (NGCHM) server.

Description

Class representing a Next Generation Clustered Heat Map (NGCHM) server.

Class representing a deployment method for a Next Generation Clustered Heat Map (NGCHM) server.

Description

Class representing a deployment method for a Next Generation Clustered Heat Map (NGCHM) server.

Class representing a Template attached to a NGCHM

Description

Class representing a Template attached to a NGCHM

Get the tiles for a shaidy dataset

Description

Get the tiles for a shaidy dataset

Usage

ngchmTileDataset(repo, dataset, rowOrder, colOrder)

Arguments

Value

a list of shaids containing the tiles

Class representing a type mapper function for Next Generation Clustered Heat Map (NGCHM).

Description

Class representing a type mapper function for Next Generation Clustered Heat Map (NGCHM).

Unregister NG-CHM Server

Description

This function unregisters a server for NG-CHM (Next-Generation Clustered Heat Map) by its UUID and optionally by its name.

Usage

ngchmUnregisterServer(uuid, name = NULL)

Arguments

Value

None. This function is used for its side effects of unregistering the server.

See Also

ngchmRegisterServer()

ngchmServer

Class representing the properties of a data point in a Next Generation Clustered Heat Map (NGCHM).

Description

Class representing the properties of a data point in a Next Generation Clustered Heat Map (NGCHM).

Class representing ngchmVersion2 object

Description

Class representing ngchmVersion2 object

Slots

name

The name under which the NGCHM will be saved to the NGCHM server.

version

Integer version number (default: 2)

format

(default: "original")

uuid

character

baggage

optCharacter

inpDir

character

outDir

character

saveDir

(default: tempdir())

propFile

(default: "chm.properties")

layers

List of data layers

colormaps

Color map

rowMenu

optList

colMenu

optList

datasets

optList

dialogs

optList

tags

optCharacter

elementMenu

optList

rowTypeFunctions

optList

colTypeFunctions

optList

elementTypeFunctions

optList

axisTypes

optList

css

optList

extrafiles

optCharacter

extrascripts

optCharacter

properties

optList

overviews

optList

javascript

optList

rowOrder

A vector, dendrogram, or function specifying the CHM row order

rowDist

Distance method to use by default RowOrder. (default: "correlation", which is 1 minus the Pearson correlation among the rows.)

rowAgglom

Agglomeration method to use by default RowOrder. Choices are those from stats::hclust. (default: "ward.D2")

colOrder

A vector, dendrogram, or function specifying the CHM column order.

colDist

Distance method to use by default ColOrder. (default: "correlation", which is 1 minus the Pearson correlation among the cols.)

colAgglom

Agglomeration method to use by default ColOrder. Choices are those from stats::hclust. (default: "ward.D2")

rowOrderMethod

character (default: "User")

colOrderMethod

character (default: "User")

rowCutLocations

Explicit list of row cut locations. If specified, rowTreeCuts is set to NULL.

rowTreeCuts

Number of tree cuts for row. If specified, rowCutLocations is set to NULL.

rowCutWidth

Width of row cuts (default: 5 rows)

rowTopItems

optCharacter

rowDisplayLength

optInteger

rowDisplayAbbreviation

optCharacter

colCutLocations

Explicit list of col cut locations. If specified, colTreeCuts is set to NULL.

colTreeCuts

Number of tree cuts for col. If specified, colCutLocations is set to NULL.

colCutWidth

Width of col cuts (defautl: 5 columns)

colTopItems

optCharacter

colDisplayLength

optInteger

colDisplayAbbreviation

optCharacter

rowMeta

optList

colMeta

optList

rowCovariateBars

optList

colCovariateBars

optList

relatedLinks

optList

relatedGroups

optList

templates

optList

width

default: 500

height

default: 500

Optional Dendrogram

Description

Optional Dendrogram

Open the NG-CHM on the specified server in the viewer.

Description

Open the NG-CHM on the specified server in the viewer.

Usage

## S3 method for class 'ngchmVersion2'
plot(x, server = NULL, viewer = NULL, ...)

Arguments

Value

No return value. The function is called for its side effect of plotting the specified NG-CHM.

Pretty Print NGCHM Type Information

Description

This function takes an object of class 'ngchm.type.info' and returns a formatted string that provides a detailed description of the NGCHM type.

Usage

## S3 method for class 'ngchm.type.info'
print(x, ...)

Arguments

Value

A string that provides a detailed description of the NGCHM type.

See Also

chmGetTypeInfo()

Print a shaidy repository

Description

Print a shaidy repository

Usage

## S3 method for class 'shaidyRepo'
print(x, ...)

Arguments

Value

The shaidy repository

Class representing the shaid of an object

Description

Class representing the shaid of an object

Add data file(s) and properties to a local shaidy repository

Description

Add data file(s) and properties to a local shaidy repository

Usage

shaidyAddFileBlob(
  shaidyRepo,
  blob.type,
  blob.file,
  filename,
  properties = NULL,
  shaid = NULL
)

Arguments

Value

The file's shaid

Determine if one more blobs exist in a shaidy repository

Description

Determine if one more blobs exist in a shaidy repository

Usage

shaidyBlobExists(repo, shaids)

Arguments

Value

a boolean vector

Copy a blob from one repository to another

Description

Copy a blob from one repository to another

Usage

shaidyCopyBlob(src, shaid, dst)

Arguments

Value

the shaid

Create a prototype blob in a shaidy repository

Description

Create a prototype blob in a shaidy repository

Usage

shaidyCreateProtoBlob(shaidyRepo, blob.type)

Arguments

Value

The file path of the prototype blob

Finalize a prototype blob

Description

Finalize a prototype blob

Usage

shaidyFinalizeProtoBlob(shaidyRepo, shaid, protoblob)

Arguments

Value

The shaid (invisibly)

The protoblob must have been created in the specified shaidy repository and with the same blob type as the shaid. When this function returns the protoblob will no longer be accessible . If a blob with the same shaid already exists in this repository, the protoblob is quitely removed without affecting the existing blob.

Find the first repository, if any, that contains the requested shaid

Description

Find the first repository, if any, that contains the requested shaid

Usage

shaidyFindRepo(repos, shaid)

Arguments

Value

The first repository containing the shaid, otherwise NULL

Get an object's component shaids

Description

Get an object's component shaids

Usage

shaidyGetComponents(object)

## S4 method for signature 'ngchm'
shaidyGetComponents(object)

## S4 method for signature 'ngchmDataset'
shaidyGetComponents(object)

## S4 method for signature 'ngchmCovariate'
shaidyGetComponents(object)

Arguments

Value

A list of shaids.

Get shaid for an object

Description

Get shaid for an object

Usage

shaidyGetShaid(object)

## S4 method for signature 'ngchm'
shaidyGetShaid(object)

Arguments

Value

The shaid of the object.

Compute the shaid to assign a protoblob

Description

Compute the shaid to assign a protoblob

Usage

shaidyHashProtoBlob(blob.type, protoblob)

Arguments

Value

The shaid to assign the protoblob

Create and initialize Shaidy Repository

Description

This function initializes a Shaidy repository in a specified directory with specified blob types.

Usage

shaidyInitRepository(shaidyDir, blob.types)

Arguments

Value

None. This function is used for its side effects of initializing the Shaidy repository.

Load the provid -> shaid DB for a local shaidy repository

Description

Load the provid -> shaid DB for a local shaidy repository

Usage

shaidyLoadProvenanceDB(shaidyDir)

Arguments

Value

A shaidyProvenanceDB

Load the provid -> labels DB for a local shaidy repository.

Description

Load the provid -> labels DB for a local shaidy repository.

Usage

shaidyLoadProvidDB(shaidyDir)

Arguments

Value

A shaidyProvidDB

Load a shaidy repository

Description

Load a shaidy repository

Usage

shaidyLoadRepository(accessMethod, shaidyDir)

Arguments

Value

A shaidyRepo

Create in memory shaid cache

Description

Create in memory shaid cache

Usage

shaidyNewCache(shaidyDir)

Arguments

Value

An in memory shaid cache

Create a provid from a list of label values

Description

Create a provid from a list of label values

Usage

shaidyProvenance(...)

Arguments

Value

A string containing the provid for the list of label values.

Get the methods for the repository API called api

Description

Get the methods for the repository API called api

Usage

shaidyRepoAPI(api)

Arguments

Value

A list of repository methods

Helper class for setting row/col gap locations as tree cuts

Description

This class is to facilitate specification of row/col gaps in chmNew(). Note: user-facing function use the term 'gap', while internal functions that interact with java programs in the NGCHM viewer project use the term 'cut'.

Slots

numberOfCuts

Integer number of cuts

See Also

chmNew()

chmTreeGaps()

Helper function to verify if variable is numeric.

Description

If not numeric, print error message and stop.

Usage

verifyNumeric(variableToCheck)

Arguments

Value

TRUE