| Type: | Package |
| Title: | Interactive Dendrograms for Visualizing Hierarchical Clusters with Prototypes |
| Version: | 0.1.0 |
| Description: | Shiny app to interactively visualize hierarchical clustering with prototypes. For details on hierarchical clustering with prototypes, see Bien and Tibshirani (2011) <doi:10.1198/jasa.2011.tm10183>. This package currently launches the application. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| Imports: | DT, dynamicTreeCut, methods, protoclust, rare, shiny, shinycssloaders, shinythemes, tools |
| Depends: | R (≥ 4.0.0) |
| RoxygenNote: | 7.1.2 |
| Suggests: | testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2022-05-17 16:03:30 UTC; andeek |
| Author: | Andee Kaplan [aut, cre], Jacob Bien [aut], Mike Bostock [cph] (Author of included d3.js library), Brian Reavis [cph] (Author of included selectize.js library) |
| Maintainer: | Andee Kaplan <andee.kaplan@colostate.edu> |
| Repository: | CRAN |
| Date/Publication: | 2022-05-18 16:30:08 UTC |
Convert a generic hclust object to a protoclust object.
Description
Convert a generic hclust object to a protoclust object.
Usage
as.protoclust(hc, protos)
Arguments
hc |
A generic hclust object using any linkage. |
protos |
A vector of prototype label indices for each branch in the dendrogram. The i-th element is the index of the prototype corresponding to the cluster formed on the i-th merge. |
Value
An object of class protoclust with a user specified vector of representative prototypes for each cluster.
This object is just like hclust but has an identical element:
merge, height, order |
identical to the values returned by |
protos |
a vector of length n - 1. The i-th element is the index of the prototype corresponding to the cluster formed on the i-th merge. |
Get an hclust object consisting of the branch with root given by a particular interior node
Description
Get an hclust object consisting of the branch with root given by a particular interior node
Usage
branch(hc, merge.id)
Arguments
hc |
protoclust object |
merge.id |
a particular interior node |
Value
an hclust object consisting of the branch with root given by merge.id.
Dataset covid19
Description
This is a protoclust object for use with protoshiny. It is the hierarchical clustering of US counties using mobility data (proportion of people staying home at least 8 hours and proportion of people going into a restaurant).
Source
https://cmu-delphi.github.io/covidcast/covidcastR/
Dynamic element of class "d3graph"
Description
Dynamic element of class "d3graph"
Usage
dynGraph(inputoutputId)
Arguments
inputoutputId |
ID of the input/output element |
Dataset faces
Description
This is a protoclust object for use with protoshiny. It is the hierarchical clustering of 400 grayscale images of faces that correspond to 10 images of 40 individuals.
Source
https://www.kaggle.com/kasikrit/att-database-of-faces
Fix uploaded files are getting renamed
Description
Fix uploaded files are getting renamed
Usage
fixUploadedFilesNames(x)
Arguments
x |
uploaded object |
Extract cluster labels
Description
Extract cluster labels
Usage
get_clusters(hc)
Arguments
hc |
A protoshiny object downloaded from the web interface. |
Value
A vector of saved cluster assignments resulting from interaction in the protoshiny application.
Get clustering of leaves from merge_id
Description
This function expects a set of node id's of a hierarchical clustering object that would define a partition of the leaves. It returns a vector giving the implied clustering of the leaves (analogous to the output of 'stats::cutree').
Usage
get_cut_from_merge_id(hc, merge_id)
Arguments
hc |
An object of class 'hclust' |
merge_id |
A numeric vector. Indexing of nodes should match that of the 'merge' matrix in an 'hclust' object. In particular, positive numbers specify interior nodes and negative numbers specify leaves. These nodes must define a partition of the leaves, meaning no node in 'merge_id' should be a descendant of another and every leaf should either be included directly or be the descendant of one of the interior nodes referenced by 'merge_id'. |
Get the labels of each interior node
Description
Get the labels of each interior node
Usage
get_nodes_to_expand_info(hc, dc)
Arguments
hc |
hclust object |
dc |
a vector of length n with integers between 0 and num_clusters such as is outputted by dynamicTreeCut::cutreeDynamicTree |
Value
Returns an (n-1)-vector giving the labels of each interior node. A positive value means that all nodes in that node's subtree have that label. A value of -1 means that this node's children have different labels. A value of -2 means that at least one child has a value of -1. And so forth.
Given a clustering get the root-to-node paths for visible nodes
Description
This function returns the binary path from root to node for each node that should be displayed in order to return the input clustering. Note that this will only be possible for a clustering 'cl' in which each cluster corresponds to a branch of 'hc'.
Usage
get_paths_from_cut(hc, cl)
Arguments
hc |
An object of class 'hclust' |
cl |
A numeric vector in the format of the output of 'stats::cutree' that gives the cluster memberships of each leaf. |
Server function
Description
Server function
Usage
get_server()
UI function
Description
UI function
Usage
get_ui()
Load an object into a new environment
Description
Load an object into a new environment
Usage
load_obj(file)
Arguments
file |
object to load into the new environment |
Dataset movies
Description
This is a protoclust object for use with protoshiny. It is the hierarchical clustering of 13,816 movies based on users' ratings and taggings of movies.
Source
https://grouplens.org/datasets/movielens/25m/
Convert a protoclust object to a JSON tree
Description
Convert a protoclust object to a JSON tree
Usage
protoclust_to_json(proto_object)
Arguments
proto_object |
protoclust object including merge, labels, and height |
Dataset seaflow
Description
This is a protoclust object for use with protoshiny. It is the hierarchical clustering of 6,336 scatterplots resulting from continuous-time flow cytometry measurements of phytoplankton.
Source
Provided by Mattias Rolf Cape and Francois Ribalet.
Dynamic element of class "select_custom"
Description
Dynamic element of class "select_custom"
Usage
selectJS(inputoutputId)
Arguments
inputoutputId |
ID of the input/output element |
Get the upper cut of a protoclust object
Description
Gets the upper part of the tree when you cut at height h (or alternately to have k leaves). Returns a valid protoclust object. This new tree has a different indexing from the original tree. i.original can be used to recover the old indexing and merge.id indicates for each leaf of new tree that had been an interior node, the merge.id of it.
Usage
upper(hc, h = NULL, k = NULL)
Arguments
hc |
protoclust object |
h |
cut height |
k |
number of leaves that upper cut should have |
Value
- hc
protoclust object representing the upper cut
- i.original
index of each element in original tree
- merge.id.leaf
merge.id from original tree of each leaf
- merge.id.interior
merge.id from original tree of each interior node
- h
cut height
- n.original
number of objects in original tree
Run a local instance of protoshiny
Description
Run a local instance of protoshiny
Usage
visualize_hc()
Value
No return value, launches the protoshiny Shiny application.
Examples
## Not run:
visualize_hc()
## End(Not run)
Dataset words
Description
This is a protoclust object for use with protoshiny. It is the hierarchical clustering of 19,599 of the most common words from Grolier's Encyclopedia.