escoheatgcn: Visualize a set of gene correlation matrix

In JINJINT/ESCO: Simple Simulation of Single-cell RNA Sequencing Data

Description

Heatmap plot a set of gene correlation matrix of the same set of genes with proper annotations

Usage

heatgcn(gcnlist, dirname = NULL, geneinfo = NULL, ord = NULL,
  maxgcn = 1, mingcn = -1, abs = FALSE, color = "-RdBu:100",
  extrainfo = NULL, ncol = 4, size = 2)

Arguments

gcnlist	a list of gene correlation matrixes of size p by p, where the rows and columns are of the same set of genes.
dirname	a string of directory names to save the plots, default as NULL, that is not saving but directly showing the plots.
geneinfo	a dataframe contains a column named 'newcelltype' of length p, where each entries corresponds to the cell group identity that a gene marks. This information will be used for annotating the final heatmap. Default is NULL, that is no annotation.
ord	a vector contains the ordering of the genes for all correlation matrix in the final heatmap. Default is NULL, that the ordering resulted from the clustering (hclust) result of the first gene correlation matrix in gcnlist.
maxgcn	the maximun cutoff of the correlation, default is 1.
mingcn	the minmum cutoff of the correlation, default is -1.
abs	whether take the absulute value of the correlation matrix or not.
color	what set of color panel to use, default is "-RdBu:100".
extrainfo	a string of extra information to saved in the final plot filename, default as "".
ncol	the number of columns in the combined plots, default as 4.
size	the size of the cellwidth and cellheight in heatmap, default as 2.

Value

heatmap plots showing immediately or pdf files saved to desinated directory.

Examples

data1 = matrix(rnorm(100),20,5)
data2 = matrix(rnorm(100),20,5)
gcnlist = lapply(list(data1,data2),function(data)gcn(data))
# heatgcn(gcnlist)

JINJINT/ESCO documentation built on May 13, 2021, 7:25 p.m.