plotRowStats {psichomics}R Documentation

Plot sample statistics per row

Description

Plot sample statistics per row

Usage

plotRowStats(data, x, y, xmin = NULL, xmax = NULL, ymin = NULL,
  ymax = NULL, xlim = NULL, ylim = NULL)

Arguments

data

Data frame or matrix

x, y

Character: statistic to calculate and display in the plot per row; choose between mean, median, var or range (or transformations of those variables, e.g. log10(var))

xmin, xmax, ymin, ymax

Numeric: minimum and maximum X and Y values to draw in the plot

xlim, ylim

Numeric: X and Y axis range

Value

Plot of data

Examples

library(ggplot2)

# Plotting gene expression data
geneExpr <- readFile("ex_gene_expression.RDS")
plotRowStats(geneExpr, "mean", "var^(1/4)") +
    ggtitle("Mean-variance plot") +
    labs(y="Square Root of the Standard Deviation")

# Plotting alternative splicing quantification
annot <- readFile("ex_splicing_annotation.RDS")
junctionQuant <- readFile("ex_junctionQuant.RDS")
psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))

medianVar <- plotRowStats(psi, x="median", y="var", xlim=c(0, 1)) +
    labs(x="Median PSI", y="PSI variance")
medianVar

rangeVar  <- plotRowStats(psi, x="range", y="log10(var)", xlim=c(0, 1)) +
    labs(x="PSI range", y="log10(PSI variance)")
rangeVar
[Package psichomics version 1.8.2 Index]