sig_heatmap {ideal} | R Documentation |
Plot a heatmap for the selected gene signature on the provided data, with the possibility to compactly display also DE only genes
sig_heatmap(vst_data, my_signature, res_data = NULL, FDR = 0.05, de_only = FALSE, annovec, title = "", cluster_rows = TRUE, cluster_cols = FALSE, center_mean = TRUE, scale_row = FALSE)
vst_data |
A |
my_signature |
A character vector, usually named, containing the genes which compose the gene signature |
res_data |
A |
FDR |
Numeric value between 0 and 1, the False Discovery Rate |
de_only |
Logical, whether to display only DE genes belonging to the pathway - defaults to FALSE |
annovec |
A named character vector, with the corresponding annotation across IDs |
title |
Character, title for the heatmap |
cluster_rows |
Logical, whether to cluster rows - defaults to TRUE |
cluster_cols |
Logical, whether to cluster column - defaults to FALSE. Recommended to be set to TRUE if de_only is also set to TRUE |
center_mean |
Logical, whether to perform mean centering on the expression values. Defaults to TRUE, as it improves the general readability of the heatmap |
scale_row |
Logical, whether to perform row-based standardization of the expression values |
A plot based on the pheatmap
function
# with the well known airway package... library(airway) data(airway) airway dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway), colData = colData(airway), design=~cell+dex) ## Not run: dds_airway <- DESeq2::DESeq(dds_airway) res_airway <- DESeq2::results(dds_airway) vst_airway <- DESeq2::vst(dds_airway) library(org.Hs.eg.db) annovec <- mapIds(org.Hs.eg.db, rownames(dds_airway),"ENTREZID","ENSEMBL") mysignatures <- read_gmt( "http://data.wikipathways.org/20190210/gmt/wikipathways-20190210-gmt-Homo_sapiens.gmt") mysignature_name <- "Lung fibrosis%WikiPathways_20190210%WP3624%Homo sapiens" library(pheatmap) sig_heatmap(vst_airway, mysignatures[[mysignature_name]], res_data = res_airway, de_only = TRUE, annovec = annovec, title = mysignature_name, cluster_cols = TRUE ) ## End(Not run)