heatmap.gg.plot: Create heatmaps for genes in clusters or conditions.

In rezakj/iCellR: Analyzing High-Throughput Single Cell Sequencing Data

Create heatmaps for genes in clusters or conditions.

Description

This function takes an object of class iCellR and genes and provides a heatmap.

Usage

heatmap.gg.plot(
  x = NULL,
  gene = "NULL",
  cell.sort = FALSE,
  data.type = "main",
  cluster.by = "clusters",
  conds.to.plot = NULL,
  min.scale = -2.5,
  max.scale = 2.5,
  interactive = TRUE,
  cex.col = 10,
  cex.row = 10,
  no.key = FALSE,
  out.name = "plot",
  heat.colors = c("blue", "white", "red")
)

Arguments

x	A data frame containing gene counts for cells.
gene	A set of gene names to be heatmapped.
cell.sort	If FALSE the cells will not be sorted based on their distance, default = TRUE.
data.type	Choose from "main", "atac", atac.imputed and "imputed", default = "main".
cluster.by	Choose from "clusters" or "none", default = "clusters".
conds.to.plot	Choose the conditions you want to see in the plot, default = NULL (all conditions).
min.scale	Set a minimum color scale, default = -2.5.
max.scale	Set a maximum color scale, default = 2.5.
interactive	If TRUE an html interactive file will be made, default = TRUE.
cex.col	Chhose a size, default = 10.
cex.row	Choose a size, default = 10.
no.key	If you want a color legend key, default = FALSE.
out.name	Output name for html file if interactive = TRUE, default = "plot".
heat.colors	Colors for heatmap, default = c("blue" ,"white", "red").

Value

An object of class iCellR

rezakj/iCellR documentation built on March 29, 2024, 6:55 p.m.