propBarplot: A plotting function for proportion by sample

In BhaktiDwivedi/GISPA: GISPA: Method for Gene Integrated Set Profile Analysis

Description

Given a gene, this function will plot the proportion of each sample over the three samples within each data type

Usage

propBarplot(gispa.output,feature,cpt,input.cex,input.cex.lab,ft.col,strip.col)

Arguments

gispa.output	: A data matrix of between gene feature profile statistics for each feature with corrosponding identified changepoints. The row names should corrospond to genes or names to be displayed on y-axis
feature	: Analysis type i.e., one ('1'), two ('2') or three ('3') dimensional feature analysis.
cpt	: Changepoints to be plotted.
input.cex	: character (or symbol expansion) for the x- and y-axis labels
input.cex.lab	: character (or symbol expansion) for the horizontal and vertial strip labels
ft.col	: a vector of colors of the bar for the features or data types
strip.col	: color to be used for the vertial strip

Details

This function expects the output from the main function of GISPA package, and highlights the gene set in the selected changepoints and their proportion in each of the three sample groups by data type.

Value

Barplot illustrating each sample proportion for each gene in the selected change point

Author(s)

Bhakti Dwivedi & Jeanne Kowalski

Examples

id <- 20 ## number of rows
s <- 3 ## number of columns
dm <- matrix(runif(id*s,0,10), nrow=id, ncol=s, 
                 dimnames=list(paste("gene", 1:id, sep=""), 
                 paste("fs", 1:s, sep="")))
changepoints <- sort(sample(1:2, id, replace=TRUE))
dm <- cbind(dm,changepoints)
propBarplot(gispa.output=dm,feature=2,cpt=1,
           input.cex=0.5,input.cex.lab=0.5,
           ft.col=c("grey0", "grey60"),strip.col="yellow")

BhaktiDwivedi/GISPA documentation built on June 23, 2020, 3:41 p.m.