plot_medians: Plot the median expression value for a set of genes using a...

In vsmuir/RNAseqTools: Tools for RNAseq analysis.

Description

This function allows you to express your love of cats.

Usage

plot_medians(
  counts, module,
  annotation, id,
  group, timepoint = NULL,
  palette, sig_comparison = NULL,
  ...)

Arguments

counts	Matrix or dataframe of counts or batch corrected residuals. The dimension corresponding to genes must have dimnames, which will be matched to the gene identifiers in gene_sets. The dimension corresponding to library or sample IDs must have dimnames, which will be matched to the sample identifiers in annotation.
module	The module or gene set, as a character vector
annotation	Dataframe where libraries that should be included in plot are in rows and phenotypic/quality characteristics are in columns.
id	Name of the column in annotation object corresponding to the library IDs used to name samples in the counts object.
group	Name of the column in annotation object corresponding to experimental groups that should be plotted.
timepoint	If NULL, data is not expected to be shown over time (default). Otherwise, the name of the column in annotation that will contain the existing time information.
sig_comparison	Argument to pass on to geom_signif. This should be a list of length-2 vectors that correspond to the group names in a pairwise comparison. These names must be present in the group column of the annotation object.
palette	The discrete color palette to be used for groups. Defaults to a 6-color scheme.
...	Optional parameters passed to gene_set_median.

Value

A plot showing the median expression values separated by experimental group, with either one element for each library in counts (if time series data was not collected) or one element for each group at each time point.

vsmuir/RNAseqTools documentation built on May 7, 2019, 8:19 a.m.