forestPlot: Compare effect sizes of a gene across all datasets in...

In MetaIntegrator: Meta-Analysis of Gene Expression Data

Description

A forest plot can be used to compare the expression values of a gene across different datasets. The size of the blue boxes is proportional to the number of samples in the study and light blue lines indicate the standard error of the effect sizes for each study (95% confidence interval). The summary effect size for all studies is indicated as yellow diamond below and the width of the diamond indicates the summary standard error.

Usage

forestPlot(metaObject, geneName, boxColor = "blue", whiskerColor = "lightblue", 
zeroLineColor = "black", summaryColor = "orange", textColor = "red")

Arguments

metaObject	a filtered metaObject, i.e. it needs to include a filterObject generated by the function filterGenes()
geneName	name of the gene for which the forest plot should be generated
boxColor	desired color for the box (default: "blue")
whiskerColor	desired color for the whiskers (default: "lightblue")
zeroLineColor	desired color for the line indicating 0 (default: "black")
summaryColor	desired color for the diamond representing the summary effect size (default: "orange")
textColor	desired color for the text of the dataset names (default: "red")

Value

Plot to compare effect sizes of a gene across datasets

Author(s)

Winston A. Haynes, Jiaying Toh

See Also

filterGenes, runMetaAnalysis, violinPlot

Examples

# compare effect sizes of the Gene1 for all discovery datasets in tinyMetaObject 
forestPlot(tinyMetaObject, geneName="Gene1")

Example output

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
[1] "character"

MetaIntegrator documentation built on March 26, 2020, 6:29 p.m.