SEPA (version 1.2.2)

truetimevisualize: truetimevisualize

Description

Visualize Gene Expression Pattern for True Experiment Time

Usage

truetimevisualize(expr, truetime, gene, mode = c("mean", "median"))

Arguments

expr

The matrix of gene expression profile.

truetime

A character data.frame or matrix of true experimental time. First column: Cell name; Second column: experiment time.

gene

A vector of gene names to be plotted.

mode

A character value specifying mean or median to be displayed

Value

A ggplot2 object.

Details

Identify the gene expression patterns for true experiment time. For the expressions of each gene, the function performs t-tests for cells from neighboring time points. The expression pattern for cells from neiboring time points could be increasing, decreasing or constant. All patterns are concatenated using "-" to form the final pattern.

Examples

data(HSMMdata)
truetimevisualize(HSMMdata,truetime,c("ENSG00000122180.4","ENSG00000125968.7"))