| Version: | 1.0 |
| Date: | 2025-05-27 |
| Title: | Three Dimensional High Throughput 'GoMiner' |
| Maintainer: | Barry Zeeberg <barryz2013@gmail.com> |
| Author: | Barry Zeeberg [aut, cre] |
| Depends: | R (≥ 4.2.0) |
| Imports: | minimalistGODB, GoMiner, HTGM, HTGM2D, grDevices, stats, R2HTML, rgl, vprint, randomGODB, stringr |
| LazyData: | true |
| LazyDataCompression: | xz |
| Description: | The Gene Ontology (GO) Consortium https://geneontology.org/ organizes genes into hierarchical categories based on biological process (BP), molecular function (MF) and cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform ontological analysis of microarray and proteomics studies, typically generating a list of significant functional categories. To capture the benefit of all three ontologies, I developed 'HTGM3D', a three-dimensional version of 'GoMiner'. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| VignetteBuilder: | knitr |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| RoxygenNote: | 7.3.2 |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2025-05-28 03:29:58 UTC; barryzeeberg |
| Repository: | CRAN |
| Date/Publication: | 2025-05-30 09:10:05 UTC |
HTGM3D
Description
compute matrix to use as input to plot3d()
Usage
HTGM3D(dir, geneList, GOGOA3, thresh1, thresh3, mn, mx, pcgMN, pcgMX, verbose)
Arguments
dir |
character string full path name to the directory acting as result repository |
geneList |
character vector of user-supplied genes of interest |
GOGOA3 |
return value of subsetGOGOA() |
thresh1 |
numerical acceptance threshold for individual ontologies |
thresh3 |
numerical acceptance threshold for joint ontology |
mn |
integer min category size threshold passed to trimGOGOA3() |
mx |
integer max category size threshold passed to trimGOGOA3() |
pcgMN |
integer param passed to pruneCatGenes |
pcgMX |
integer param passed to pruneCatGenes |
verbose |
integer vector representing vprint classes |
Value
returns matrix containing information that provides the input needed for running plot3d()
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# you can generate it using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/tree/main/databases
load("/Users/barryzeeberg/personal/GODB_RDATA/goa_human/GOGOA3_goa_human.RData")
geneList<-cluster52
dir<-tempdir()
mat3d<-HTGM3D(dir,geneList,GOGOA3,thresh1=3,thresh3=3,mn=2,
mx=10000,pcgMN=2,pcgMX=200,verbose=1:5)
## End(Not run)
HTGM3Ddriver
Description
driver to invoke HTGM3D()
Usage
HTGM3Ddriver(
dir,
geneList,
GOGOA3,
thresh1,
thresh3,
mn,
mx,
pcgMN,
pcgMX,
verbose
)
Arguments
dir |
character string full path name to the directory acting as result repository |
geneList |
character vector of user-supplied genes of interest |
GOGOA3 |
return value of subsetGOGOA() |
thresh1 |
numerical acceptance threshold for individual ontologies |
thresh3 |
numerical acceptance threshold for joint ontology |
mn |
integer min category size threshold passed to trimGOGOA3() |
mx |
integer max category size threshold passed to trimGOGOA3() |
pcgMN |
integer param passed to pruneCatGenes |
pcgMX |
integer param passed to pruneCatGenes |
verbose |
integer vector representing vprint classes |
Details
suggested standardized class codes for vprint() -1 = developer debugging only 0 = constitutively turned on 1 = help for new user 2 = follow progress of long computation 3 = primary results 4 = meta information (e.g. dims of a matrix before and after trimming) 5 = warnings 6 = errors
Value
returns matrix containing information that provides the input needed for running plot3d()
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# you can generate it using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/tree/main/databases
load("/Users/barryzeeberg/personal/GODB_RDATA/goa_human/GOGOA3_goa_human.RData")
#load("data/cluster52.RData")
geneList<-cluster52
dir<-tempdir()
l3<-HTGM3Ddriver(dir,geneList,GOGOA3,thresh1=3,thresh3=3,
mn=2,mx=20000,pcgMN=2,pcgMX=200,verbose=1:5)
## End(Not run)
HTGM3D data set
Description
HTGM3D data set
Usage
data(Housekeeping_Genes)
Jaccard3
Description
compute the number of genes in the intersection of categories from 3 ontology branches
Usage
Jaccard3(dir, m, thresh1 = 3, thresh3 = 3, verbose = 2)
Arguments
dir |
character string full path name to the directory acting as result repository |
m |
return value of pruneCatGenes() |
thresh1 |
parameter passed to Jaccard3() |
thresh3 |
parameter passed to Jaccard3() |
verbose |
integer vector representing vprint classes |
Value
returns matrix tabulating genes in the intersection of categories from 3 ontology branches also has side effect of saving files containing those genes
Examples
#load("data/x_m11.RData")
Jaccard3(tempdir(),x_m11,thresh1=3,thresh3=3,verbose=1:5)
blackBodyRadiationColors
Description
set up color scale for black body spectrum
Usage
blackBodyRadiationColors(x, max_value = 1)
Arguments
x |
numeric should be between 0 (black) and 1 (white) |
max_value |
numeric maximum value to be used for scaling |
Details
I obtained this by copy and paste from internet (reference unknown)
Value
returns no value, but has side effect of generating color map
Examples
colors.blackBody <- rev(blackBodyRadiationColors(seq(0.3,1,length.out=20)))
catNum3
Description
assign the axis coordinate number to be used for the plotting position for each category
Usage
catNum3(l)
Arguments
l |
list each component corresponds to an ontology branch, and contains the decreasing sorted tabulation of output of the number of times that a category appears in a triplet |
Details
a component of l is like: GO_0005515__protein_binding GO_0042802__identical_protein_binding GO_0005178__integrin_binding 38 4 3
#' a component of l1 is like: GO_0005515__protein_binding GO_0042802__identical_protein_binding GO_0005178__integrin_binding 1 2 3
Value
returns a list each component corresponds to an ontology branch, and contains a vector of category plotting positions
Examples
#load("data/x_l.RData")
catNum3(x_l)
HTGM3D data set
Description
HTGM3D data set
Usage
data(cluster52)
graphIt
Description
annotate a selected point in the 3d graphic
Usage
graphIt(mat3d, sp, w, r, verbose)
Arguments
mat3d |
component of HTGM3Ddriver() output list |
sp |
integer vector containing c(x,y,z) coordinated of point |
w |
integer line number within mat3d |
r |
numeric max value of x,y,z ranges |
verbose |
integer vector representing vprint classes |
Value
returns no value, but has side effect of annotating the 3D graph
insertCatSize
Description
compute fraction of total genes in the entire ontology that map to each category, and insert column into matrix mat
Usage
insertCatSize(mat, GOGOA3)
Arguments
mat |
return value of Jaccard3() |
GOGOA3 |
return value of subsetGOGOA() |
Value
returns augmented version of matrix mat
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# you can generate it using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/tree/main/databases
load("/Users/barryzeeberg/personal/GODB_RDATA/goa_human/GOGOA3_goa_human.RData")
mat2<-insertCatSize(x_mat,GOGOA3)
## End(Not run)
interactWithGraph3D
Description
rotate the 3d graph and/or select a point within the 3D graph, and annotate that point
Usage
interactWithGraph3D(mat3d, maxfract = 1, newWindow = TRUE, verbose = TRUE)
Arguments
mat3d |
component of HTGM3Ddriver() output list |
maxfract |
numeric upper threshold for category size to display |
newWindow |
Boolean if TRUE open new window to avoid over writing current window |
verbose |
integer vector representing vprint classes |
Value
returns no value, but has side effect of annotating the 3D graph
Examples
if(interactive()){
#load("data/x_mat3d.RData")
interactWithGraph3D(x_mat3d)
}
plot3Dmat
Description
compute x,y,z coordinates for each triplet
Usage
plot3Dmat(mat, l)
Arguments
mat |
return value of HTGM3D() |
l |
return value of catNum3() |
Value
augmented version of matrix containing x,y,z coordinates for each triplet
Examples
#load("data/x_mat.RData")
#load("data/x_l.RData")
p3<-plot3Dmat(x_mat,x_l)
pruneCatGenes
Description
eliminate those categories to which no genes map
Usage
pruneCatGenes(m, mn = 2, mx = 200)
Arguments
m |
the return value of catGenes() |
mn |
integer min category size threshold passed to trimGOGOA3() |
mx |
integer max category size threshold passed to trimGOGOA3() |
Value
returns pruned version of matrix m
Examples
#load("data/x_cg.RData")
m<-pruneCatGenes(x_cg,2,200)
showGenes
Description
open gene list in a textEdit window
Usage
showGenes(mat3d, w, range, npad)
Arguments
mat3d |
component of HTGM3Ddriver() output list |
w |
integer line number within mat3d |
range |
list of ranges |
npad |
integer number of blanks for padding |
Value
returns no value, but has side effect of opening textEdit
subMatDiffs
Description
retrieve submatrices of common rownames and colnames, and report differences
Usage
subMatDiffs(m1, m2, verbose = 3)
Arguments
m1 |
matrix |
m2 |
matrix |
verbose |
integer vector representing vprint classes |
Details
compare submatrices of m1 and m2 that have common rownames and colnames
Value
returns no values
Examples
rn<-c("a","b","c")
cn<-c("a","b","c","d")
m1<-matrix(1:12,nrow=length(rn),ncol=length(cn))
rownames(m1)<-rn
colnames(m1)<-cn
m2<-m1
subMatDiffs(m1,m2)
m3<-m1
m3[1,1]<-0
m3[1,2]<-0
subMatDiffs(m1,m3)
m4<-m3
colnames(m4)<-c("aa","b","c","d")
subMatDiffs(m1,m4)
HTGM3D data set
Description
HTGM3D data set
Usage
data(x_cg)
HTGM3D data set
Description
HTGM3D data set
Usage
data(x_l)
HTGM3D data set
Description
HTGM3D data set
Usage
data(x_m11)
HTGM3D data set
Description
HTGM3D
Usage
data(x_mat)
HTGM3D data set
Description
HTGM3D
Usage
data(x_mat3d)