heatmapcell: heatmapcell

In SMDIC: Identification of Somatic Mutation-Driven Immune Cells

heatmapcell

Description

A function to draw clustered heatmaps for the cells driven by a somatic mutation.

Usage

heatmapcell(
  gene,
  mutcell,
  cellmatrix,
  mutmatrix,
  title = NA,
  show_rownames = TRUE,
  show_colnames = FALSE,
  annotation_colors = NA,
  annotation_row = NA,
  annotation_col = NA,
  color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100)
)

Arguments

gene	Somatic mutant gene name
mutcell	A list, mutcell is the result of function 'mutcorcell'.
cellmatrix	Cell abundance matrix, cellmatrix is the result of function 'exp2cell'.
mutmatrix	A binary mutations matrix, which can not only come from the maf2matrix function, but also any binary mutations matrix, in which 1 represents any mutation occurs in a particular gene in a particular sample, otherwise the element is 0.
title	The title of the plot
show_rownames	boolean specifying if column names are be shown.
show_colnames	boolean specifying if column names are be shown.
annotation_colors	list for specifying annotation_row and annotation_col track colors manually. It is possible to define the colors for only some of the features. Check examples for details.
annotation_row	data frame that specifies the annotations shown on left side of the heatmap. Each row defines the features for a specific row. The rows in the data and in the annotation are matched using corresponding row names. Note that color schemes takes into account if variable is continuous or discrete.
annotation_col	similar to annotation_row, but for columns.
color	vector of colors used in heatmap.

Examples

#get the result of `mutcorcell` function.
mutcell<-GetExampleData("mutcell")

#get cell abundance matrix which is the result of exp2cell function
cellmatrix<-GetExampleData("cellmatrix")

#get the binary mutations matrix
mutmatrix<-GetExampleData("mutmatrix")

# plot significant up-regulation or down-regulation cells heat map specific for breast cancer
heatmapcell(gene = "TP53",mutcell = mutcell,cellmatrix = cellmatrix,mutmatrix = mutmatrix)

SMDIC documentation built on Oct. 18, 2024, 9:07 a.m.