heatmapcell: heatmapcell

Description Usage Arguments Examples

View source: R/visualization.R

Description

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

Usage

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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

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#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 Nov. 13, 2020, 5:06 p.m.