expHeatmap: Expression heatmap

In tomoda: Tomo-seq data analysis

Description

Heatmap for gene expression across sections in a SummarizedExperiment object.

Usage

expHeatmap(object, genes, matrix = "scaled", size = 5)

Arguments

object	A SummarizedExperiment object.
genes	A vector of character, the name of genes to plot heatmap.
matrix	Character, must be one of "count", "normalized", or "scaled".
size	Character, the size of gene names. Set it to 0 if you do not want to show gene names.

Value

A ggplot object.

Examples

data(zh.data)
zh <- createTomo(zh.data)

# Plot some genes.
expHeatmap(zh,
 c("ENSDARG00000002131", "ENSDARG00000003061", "ENSDARG00000076075", "ENSDARG00000076850"))

# Plot peak genes.
peak_genes <- findPeakGene(zh)
expHeatmap(zh, peak_genes$gene)

# Remove gene names if too many genes are in the heatmap.
expHeatmap(zh, peak_genes$gene, size=0)

tomoda documentation built on Nov. 8, 2020, 8:10 p.m.