plotStratifyBy {variancePartition} | R Documentation

## 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)

[Package variancePartition version 1.10.4 Index]