truetimevisualize: truetimevisualize

In SEPA: SEPA

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

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.

Value

A ggplot2 object.

Author(s)

Zhicheng Ji, Hongkai Ji <[e-mail]>

Examples

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

SEPA documentation built on May 6, 2019, 2:42 a.m.