SEPA (version 1.2.2)

pseudotimevisualize: pseudotimevisualize

Description

Visualize Gene Expression Pattern for Pseudo Temporal Cell Ordering

Usage

pseudotimevisualize(pattern, gene, showtrue = F)

Arguments

pattern

The exact output of the pseudotimepattern function.

gene

A character value or vector of gene names. Should be included in the gene expression matrix.

showtrue

For the heatmap of multiple gene, whether to display true gene expression values or fitted gene expression values.

Value

A ggplot2 object

Details

Visualize gene expression pattern of one or multiple genes for pseudo temporal cell ordering. For one gene, a scatterplot with fitted lines will be generated. For multiple genes, a heatmap with fitted or true expression values will be generated.

Examples

data(HSMMdata)
pattern <- pseudotimepattern(HSMMdata,pseudotime)
pseudotimevisualize(pattern,"ENSG00000108821.9")
pseudotimevisualize(pattern,c("ENSG00000108821.9","ENSG00000187193.8"))