PlotCountHeatmap: Plotting logged expression distribution

In YosefLab/SymSim: Simulate Single Cell RNA Sequencing Data

Plotting logged expression distribution

Description

takes an expression matrix and makes a 2D histogram on the log scale where each row is a gene and the number of samples in a bin is shown by the intensity of the color

Usage

PlotCountHeatmap(
  log_real,
  mean_counts,
  data_name,
  given_ord = NA,
  zeropropthres = 0.8,
  filename = NA,
  saving = F
)

Arguments

log_real	the logged distribution of count distribution, obtained through the LogDist function
mean_counts	the average expression for each gene, used for sorting purpose
data_name	a string which is included in the title of the plot to describe the data used
given_ord	the given order of genes
zeropropthres	the genes with zeroproportion greater than this number is not plotted (default to 0.8)
filename	the name of the output plot. Will not be used if saving=F.
saving	if the plot should be saved into a file

Examples

 
heatmapplot <- PlotCountHeatmap(LogDist(countmatrix,seq(0, 4, 0.4)),rowMeans(countmatrix),
given_ord= NA,zeropropthres=1,filename=NA,data_name='true counts',saving=F)
heatmapplot[[2]]

YosefLab/SymSim documentation built on Sept. 30, 2024, 2:22 p.m.