heatmapPlot {rrvgo} | R Documentation |
heatmapPlot Plot similarity matrix as a heatmap
heatmapPlot( simMatrix, reducedTerms = NULL, annotateParent = TRUE, annotationLabel = "parentTerm", ... )
simMatrix |
a (square) similarity matrix. |
reducedTerms |
a data.frame with the reduced terms from reduceSimMatrix() |
annotateParent |
whether to add annotation of the parent |
annotationLabel |
display "parent" ids or "parentTerm" string |
... |
other parameters sent to pheatmap::pheatmap() |
Matrix with similarity scores between terms is represented as a heatmap.
Invisibly a pheatmap object that is a list with components
go_analysis <- read.delim(system.file("extdata/example.txt", package="rrvgo")) simMatrix <- calculateSimMatrix(go_analysis$ID, orgdb="org.Hs.eg.db", ont="BP", method="Rel") scores <- setNames(-log10(go_analysis$qvalue), go_analysis$ID) reducedTerms <- reduceSimMatrix(simMatrix, scores, threshold=0.7, orgdb="org.Hs.eg.db") heatmapPlot(simMatrix, reducedTerms, annotateParent=TRUE, annotationLabel="parentTerm", fontsize=6)