Description Usage Arguments Value Author(s) See Also Examples
View source: R/post_analysis.R
Clusters the samples and the genes associated with a GO term using the expression levels of genes related to a given ontology. Represents expression levels of those genes in a heatmap.
1 2 3 4 5 6 7 8 9 10 11 12 13 | heatmap_GO(
go_id, result, eSet, f=result$factor, subset=NULL, gene_names=TRUE,
NA.names=FALSE, margins=c(7 ,5),
scale="none", cexCol=1.2, cexRow=0.5,
labRow=NULL,
cex.main=1, trace="none", expr.col=bluered(75),
row.col.palette="Accent",
row.col=c(),
main=paste(
go_id, result$GO[result$GO$go_id == go_id,"name_1006"]
),
main.Lsplit=NULL,
...)
|
go_id |
A Gene Ontology (GO) identifier. |
result |
The output of |
eSet |
|
f |
The grouping factor in |
subset |
A named list to subset |
gene_names |
A boolean value. Default is TRUE, to label genes by their associated gene name. If FALSE, labels the genes by their feature identifier in the expression dataset (i.e. Ensembl gene identifier or microarray probeset). |
NA.names |
A boolean value. Default is TRUE. If labelling genes by their associated
gene name (see argument |
margins |
A numeric vector of length 2 specifying the number of lines of margins to
apply for the bottom and right margins, respectively.
Defaults are 7 (bottom) and 5 (right). For Ensembl gene identifiers, we
suggest setting manually a bottom margin of 13. See |
scale |
Character indicating if the values should be centered and scaled in either
the row direction or the column direction, or none. Default is "none".
See |
cexCol, cexRow |
Positive numbers, used as cex.axis in for the row or column axis labeling.
Defaults are 1.2 and 1, respectively. See |
labRow |
A character vector of names to re-label the rows (samples).
If vector of length 1, it is assumed to be a column name in the
|
cex.main |
Scaling factor of the main title font size. Default is 1. We suggest to
use it in combination with the argument |
trace |
Character string indicating whether a solid "trace" line should be drawn across each 'row' or down each 'column', both' or 'none'. The distance of the line from the center of each color-cell is proportional to the size of the measurement. Defaults to 'none'. |
expr.col |
Character vector indicating the colors to represent the different levels
of gene expression. Defaults to a colormap of 75 shades ranging from blue
(low) to red (high) and centered around white. If using differential
expression data, you should probably use |
row.col.palette |
A valid |
row.col |
A vector of color names or codes. The number of colors provided must match the number of levels of the grouping factor. Default to an palette of up to 9 colors marking the different levels of the predefined grouping factor on the left side of the heatmap. |
main |
Main title of the figure. Default is paste(go_id, go_name). |
main.Lsplit |
Number of characters after which a new-line character will be inserted in the main title. If this would occur within a word, the new-line character will be inserted before this word. Default is NULL, leaving the title on a single line. |
... |
Additional arguments passed on to |
Returns the output of the heatmap.2()
function.
Kevin Rue-Albrecht
Method heatmap.2
,
GO_analyse
,
and brewer.pal.info
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # load the sample output data
data(AlvMac_results)
# Heatmap the top-ranked GO term (toll-like receptor 4 signaling pathway) as
# example
heatmap_GO(go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac)
# Same with larger sample labels on the right hand side.
heatmap_GO(go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac, cexRow=1)
# Change the color-coding to green-black-red gradient (more appropriate for
# differential expression values)
library(gplots)
heatmap_GO(
go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac,
expr.col=greenred(75)
)
|
Loading required package: grid
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
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