variancePartition (version 1.2.5)

plotStratifyBy: plotStratifyBy

Description

Plot gene expression stratified by another variable

Usage

plotStratifyBy(geneExpr, xval, yval, xlab = xval, ylab = yval, main = NULL, sortBy = xval, colorBy = xval, sort = TRUE, text = NULL, text.y = 1, text.size = 5, pts.cex = 1, ylim = NULL, legend = TRUE, x.labels = FALSE)

Arguments

geneExpr

data.frame of gene expression values and another variable for each sample. If there are multiple columns, the user can specify which one to use

xval

name of column in geneExpr to be used along x-axis to stratify gene expression

yval

name of column in geneExpr indicating gene expression

xlab

label x-asis. Defaults to value of xval

ylab

label y-asis. Defaults to value of yval

main

main label

sortBy

name of column in geneExpr to sort samples by. Defaults to xval

colorBy

name of column in geneExpr to color box plots. Defaults to xval

sort

if TRUE, sort boxplots by median value, else use default ordering

text

plot text on the top left of the plot

text.y

indicate position of the text on the y-axis as a fraction of the y-axis range

text.size

size of text

pts.cex

size of points

ylim

specify range of y-axis

legend

show legend

x.labels

show x axis labels

Value

ggplot2 object

Examples

# load library
# library(variancePartition)

# load simulated data:
data(varPartData)

# Create data.frame with expression and Tissue information for each sample
GE = data.frame( Expression = geneExpr[1,], Tissue = info$Tissue)

# Plot expression stratified by Tissue
plotStratifyBy( GE, "Tissue", "Expression")

# Omit legend and color boxes grey
plotStratifyBy( GE, "Tissue", "Expression", colorBy = NULL)

# Specify colors
col = c( B="green", A="red", C="yellow")
plotStratifyBy( GE, "Tissue", "Expression", colorBy=col, sort=FALSE)