plotGenes: Simple function to plot gene expression

Description Usage Arguments

View source: R/plotGenes.R

Description

Simple function to plot individual gene expression for a number of genes

Usage

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plotGenes(x, center = TRUE, scale = TRUE, labels = NULL,
  xval = NULL, sel = NULL, aveby = NULL, xlim = NULL,
  ylim = NULL, col = "#33333366", sdcol = NULL, lwd = 1,
  add = FALSE, las = 2, genelabels = rownames(x), debug = FALSE,
  xlab = "", ylab = "", hline = 0, vlines = T, ...)

Arguments

x

A matrix containing gene expression data (row-wise: genes; col-wise: samples)

center

Whether gene expressions should be centered to mean= 0

scale

Whether gene expressions should be scaled to sd= 1

labels

Labels for the x-axis

xval

Values for the x-axis

sel

Selection of rows from the matrix to display

aveby

If there are replicates that should be averaged before plotting, this vector should contain IDs unique for a batch, but identical between replicates in a batch, of length equal to number of columns in x

xlim, ylim

limits for x- and y- axes

col

default color to use in plotting

sdcol

color used to plot the standard deviations if aveby is not NULL

lwd

default line width to use in plotting

add

Whether the existing plot should be updated rather than replaced

las

use las=2 to make sure x-axis labels are vertical

genelabels

labels shown on the left for each gene plotted. Must have a length equal to number of rows in x.

debug

Switch on debugging

xlab

Label for the x axis

ylab

Label for the y axis

hline

Whether a grey line should be drawn at h=0

vlines

Whether grey vertical lines should be drawn at each sample

...

Additional parameters will be passed to plot


january3/myfuncs documentation built on April 1, 2020, 4:42 a.m.