plotDensity: Density plots of columns in a matrix

In QuackenbushLab/yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Density plots of columns in a matrix

Description

Plots the density of the columns of a matrix. Wrapper for matdensity.

Usage

plotDensity(obj, groups = NULL, normalized = FALSE, legendPos = NULL, ...)

Arguments

obj	ExpressionSet object
groups	Vector of labels for each sample or a column name of the phenoData slot for the ids to filter. Default is the column names.
normalized	TRUE / FALSE, use the normalized matrix or log2-transformed raw counts
legendPos	Legend title position. If null, does not create legend by default.
...	Extra parameters for matdensity.

Value

A density plot for each column in the ExpressionSet object colored by groups

Examples

data(skin)
filtData <- filterLowGenes(skin,"SMTSD")
plotDensity(filtData,groups="SMTSD",legendPos="topleft")
# to remove the legend
plotDensity(filtData,groups="SMTSD")

QuackenbushLab/yarn documentation built on March 7, 2024, 3:53 p.m.