plotStratify {variancePartition} | R Documentation

## plotStratify

### Description

Plot gene expression stratified by another variable

### Usage

    plotStratify(formula, data, xlab, ylab, main, sortBy, colorBy,
      sort = TRUE, text = NULL, text.y = 1, text.size = 5,
      pts.cex = 1, ylim = NULL, legend = TRUE, x.labels = FALSE)

### Arguments

`formula` | specify variables shown in the x- and y-axes. Y-axis should be continuous variable, x-axis should be discrete.
`data` | data.frame storing continuous and discrete variables specified in formula
`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

    # Note: This is a newer, more convient interface to plotStratifyBy()

    # 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
    plotStratify( Expression ~ Tissue, GE )

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

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

[Package variancePartition version 1.12.3 Index]