M3DropExpressionHeatmap {M3Drop}R Documentation

Plot Heatmap of Gene Expression

Description

Plots a customized heatmap of scaled log expression values.

Usage

  M3DropExpressionHeatmap(genes, expr_mat, cell_labels=NA, interesting_genes=NA, key_genes=genes, key_cells=NA)

Arguments

genes

a character vector of gene names to be plot.

expr_mat

a numeric matrix of normalized (not log-transformed) expression values, columns = samples, rows = genes.

cell_labels

factor of labels for each cell in the expression matrix that will be used to coloured in a top bar of the heatmap.

interesting_genes

list of vectors of gene names that will be used to colour the bar to the left of the heatmap.

key_genes

a character vector of gene names to be labelled on the heatmap.

key_cells

a character vector of cells to be labelled on the heatmap. Unlabelled cells will be assigned a numerical index

Details

Modifies the gplots function heatmap.2 to replace the row dendrogram with a legend of the colours used in the columns colour bar (cell_labels) and use a custom colour scalling. Expression is displayed as Z-scores of log transformed expression (adding a pseudocount of 1) coloured blue-white-red centered at 0 and binned in the range [-2,2].

Value

Invisibly, output from heatmap.2 call.

Examples

  library(M3DExampleData)
  M3DropExpressionHeatmap(head(rownames(Mmus_example_list$data),20),Mmus_example_list$data, cell_labels = Mmus_example_list$labels)

[Package M3Drop version 1.8.1 Index]