plotStratifyBy
Plot gene expression stratified by another variable
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 )
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 |
ggplot2 object
# 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)
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