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

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Create heatmaps for genes in clusters or conditions.

Description

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

Usage

heatmap.gg.plot(x = NULL, gene = "NULL", cluster.by = "clusters",
  min.scale = -2.5, max.scale = 2.5, interactive = T, 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.
cluster.by	Choose from "clusters" or "conditions", defult = "clusters".
interactive	If TRUE an html intractive file will be made, defult = TRUE.
no.key	If you want a color legend key defult = FALSE.
out.name	Output name for html file if interactive = TRUE defult = "plot".
heat.colors	Colors for heatmap, defult = c("blue" ,"white", "red").

Value

An object of class scSeqR

Examples

## Not run: 
heatmap.gg.plot(my.obj, gene = MyGenes, interactive = T, out.name = "plot", cluster.by = "clusters")

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.