cpmThresh: Plot CPM Thresh

In weshorton/wrh.rUtils: Miscellaneous R Utility Functions

Plot CPM Thresh

Description

Plot the cpm counts for a dataset to determine a potential filter threshold.

Usage

cpmThresh(
  raw_dt,
  cpm_dt,
  metaCols_v = "Gene",
  rawTest_v = c(10, 20, 30),
  indPlot_v = F,
  histPlot_v = T,
  densPlot_v = T,
  boxPlot_v = T,
  plotDir_v = NA,
  meta_dt,
  plotCols_lsv = list()
)

Arguments

raw_dt	data.table of raw values. rows = genes; columns = samples.
cpm_dt	data.table of cpm values. rows = genes; columns = samples.
metaCols_v	columns that should not be used for cpm values. Default is "Gene"
rawTest_v	vector of numbers to use as raw values to test for cpm equivalents.
indPlot_v	logical. TRUE - print raw-cpm comparison plot for each sample; FALSE - do not print plot.
histPlot_v	logical. TRUE - print summary histogram plot; FALSE - do not print
densPlot_v	logical. TRUE - print density plot; FALSE - do not print
boxPlot_v	logical. TRUE - print boxplot; FALSE - do not print
plotDir_v	character vector of where to save plots.
meta_dt	data.table containing metadata information. Should have column named "sample" that matches colnames of raw_dt/cpm_dt
plotCols_lsv	list of metadata columns to use to change plots. list element name is the plotting parameter (e.g. color or fill), while list element value is the column name (e.g. batch, treatment)

Value

Named vector where values are cpm and names are the corresponding raw value.

weshorton/wrh.rUtils documentation built on Oct. 28, 2024, 7:24 a.m.