plotGA {MetaCyto} | R Documentation

## Plot the result from the glmAnalysis function

### 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)

[Package MetaCyto version 1.4.0 Index]