plotStratifyBy: plotStratifyBy

In variancePartition: Quantify and interpret divers of variation in multilevel gene expression experiments

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)

variancePartition documentation built on Nov. 8, 2020, 5:18 p.m.