heatGenes: HeatGenes: Heatmap of your genes of interest!

In perllb/deseqAbstraction: A set of functions to make DESeq pipes more smooth

HeatGenes: Heatmap of your genes of interest!

Description

Plots heatmap showing the expression of the genes of given gene-list and having sd above given value

Usage

heatGenes(data, genes, a1 = NULL, a2 = NULL, n1 = NULL, n2 = NULL,
  sd = 0.001, z = FALSE, cluster_col = T, cluster_row = T,
  k = NA, cutreeR = 1, cutreeC = 1, redBlue = T, breaks = NA)

Arguments

data:	deseq matrix data (with varianceStablizing, rlog etc - eg. assay(vsd)
genes:	a vector of gene IDs to be extracted from rownames of data
a1:	annotation of the samples
a2:	annotation of the samples
n1:	name of annotation in a1
n2:	name of annotation in a2
sd:	standard deviation cutoff for heatmap
z:	logical operator. if TRUE, normalize by row (z-score). if FALSE (default), then plot normalized expression values
cluster_col:	logical operator: if TRUE (default), cluster columns, if FALSE do not cluster columns
cluster_row:	logical operator: if TRUE (default), cluster rows, if FALSE do not cluster
k:	number of clusters in k-means
cutreeR:	number of cuts in rowtree
cutreeC:	number of cuts in Coltree

Examples

vst <- varianceStabilizingTransformation(dds)
genes <- c("TRIM28","DNMT1","ZNF52")
heatGenes(data = assay(vst),genes = genes, sd = 1, a1 = colData$cellLine, a2 = colData$treatment,n1 = "Cell Line",n2 = "Treatment",z = T)

perllb/deseqAbstraction documentation built on Oct. 31, 2023, 2:13 a.m.