heatmap.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.plot(x = NULL, gene = "NULL", cluster.by = "clusters",
  cluster.rows = F, 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".
cluster.rows	If set to FALSE the genes would not be clustered, defult = TRUE.
heat.colors	Colors for heatmap, defult = c("blue" ,"white", "red").
scale	Choose from "row" or "column", defult = "row".

Value

An object of class scSeqR

Examples

## Not run: 
MyGenes <- c("SOD1","CD7")
MyGenes <- top.markers(marker.genes, topde = 10, min.base.mean = 0.8)
heatmap.plot (my.obj, gene = MyGenes, cluster.by = "clusters", cluster.rows = T)

## End(Not run)

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