exprMean: Mean expression heatmaps

In e-myers/rnaseq: Process, Analyze and Visualize RNA-seq Data

Description

Create single column heatmap of mean expression values (across samples) Needs plotly

Usage

exprMean(exprDataFrame, genes = NULL, samples = NULL, L2 = FALSE,
  yticklabSize = 8, figHeightPerGene = 20, figWidth = 200,
  colorsPlot = colorRamp(c("turquoise1", "magenta")), ncolors = 5,
  plotTitle = NULL, minVal = NULL, maxVal = NULL, fileOut = NULL)

Arguments

exprDataFrame	Data frame - Gene x sample expression values (counts, tpm, whatever)
genes	Character - Gene symbols that appear as row names in exprDataFrame
samples	Character - Sample names that appear as column names in exprDataFrame
L2	Logical - Whether to take log2 of values
yticklabSize	Numeric - Font size for gene symbols
figHeightPerGene	Numeric -
figWidth	Numeric -
colorsPlot	Color ramp -
ncolors	Numeric -
plotTitle	String -
minVal	Numeric -
maxVal	Numeric -
fileOut	String - If given, save png to with this filename

Details

Given a gene-by-sample dataframe with expression values, and (optionally) a list of the genes and samples you want included, make a one-column heatmap of mean expression using plotly. Note that, probably because I'm not set up to do the paying thing, some stuff doesn't get incorporated into the output png.

Value

Plotly object

Author(s)

Emma Myers

e-myers/rnaseq documentation built on May 20, 2019, 9:14 p.m.