plotGA: Plot the result from the glmAnalysis function

In hzc363/MetaCyto: MetaCyto: A package for meta-analysis of cytometry data

Description

A function that plots the result from the glmAnalysis function.

Usage

plotGA(GA, size = 16)

Arguments

GA	A data frame returned from the function glmAnalysis.
size	The font size of texts in the plot

Value

The plot will show up automatically.

Examples

library(dplyr)
#collect all summary statistics
fn=system.file("extdata","",package="MetaCyto")
files=list.files(fn,pattern="cluster_stats_in_each_sample",recursive=TRUE,
                full.names=TRUE)
fcs_stats=collectData(files,longform=TRUE)
# Collect sample information
files=list.files(fn,pattern="sample_info",recursive=TRUE,full.names=TRUE)
sample_info=collectData(files,longform=FALSE)
# join the cluster summary statistics with sample information
all_data=inner_join(fcs_stats,sample_info,by="fcs_files")
# See the fraction of what clusters are affected
# by age (while controlling for Gender)
GA=glmAnalysis(value="value",variableOfInterst="Subject Age",
             parameter="fraction",
              otherVariables=c("Gender"),studyID="study_id",label="label",
              data=all_data,CILevel=0.95,ifScale=c(TRUE,FALSE))
GA=GA[order(GA$Effect_size),]
# plot the effect sizes
plotGA(GA)

hzc363/MetaCyto documentation built on July 27, 2020, 2:46 a.m.