escoheatdata: Visualize a set of gene expression matrix

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

Description

Heatmap plot a set of gene expression matrix of the same set of gene and cells with proper annotations

Usage

heatdata(datalist, dirname = NULL, genes = NULL, cellinfo = NULL,
  rowv = FALSE, colv = FALSE, geneinfo = NULL, log = TRUE,
  norm = TRUE, maxdata = NULL, mindata = 0, ncol = 3, size = 3,
  width = 8, height = 8, color = "YlGnBu:100", extrainfo = "")

Arguments

datalist	a list of gene expression matrixes of size p by n, (where rows are of the same set of genes and columns are of the same set of cells).
dirname	a string of directory names to save the plots, default as NULL, that is not saving but directly showing the plots.
genes	a vector contains names of the genes to be plotted.
cellinfo	a dataframe contains a column named 'newcelltype' of length n, where each entries corresponds to the cell group identity that a cell belongs to. This information will be used for annotating the final heatmap. Default is NULL, that is no cell annotation.
rowv	a vector contains the ordering of the genes for all data matrix in the final heatmap. Default is FALSE, that the ordering resulted from the clustering (hclust) result of the first data matrix in datalist.
colv	a vector contains the ordering of the cells for all data matrix in the final heatmap. Default is FALSE, that the ordering resulted from the clustering (hclust) result of the first data matrix in datalist.
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 gene annotation.
log	whether take the log transform of the data
norm	whether take the counts per million normalization of the data
maxdata	the maximun cutoff of the correlation, default is NULL, that is no cutoff.
mindata	the minmum cutoff of the correlation, default is 0.
ncol	the number of columns in the combined plots, default as 3.
size	the size of the cellwidth and cellheight in heatmap, default as 3.
width	the width of the final pdf plot, default as 8.
height	the height of the final pdf plot, default as 8.
color	what set of color panel to use, default is "YlGnBu:100".
extrainfo	a string of extra information to saved in the final plot filename, default as "".

Value

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

Examples

data = matrix(rnorm(100),20,5)
# heatdata(list(data))

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