plotFiltering: Visualize the filtering procedure

In fmicompbio/mutscan: Preprocessing and Analysis of Deep Mutational Scanning Data

Visualize the filtering procedure

Description

Display the number (or fraction) of reads remaining after each step of the internal mutscan filtering.

Usage

plotFiltering(
  se,
  valueType = "reads",
  onlyActiveFilters = TRUE,
  displayNumbers = TRUE,
  numberSize = 4,
  plotType = "remaining",
  facetBy = "sample"
)

Arguments

se	A SummarizedExperiment object, e.g. from summarizeExperiment.
valueType	Either "reads" or "fractions", indicating whether to plot the number of reads, or the fraction of the total number of reads, that are retained after/filtered out in each filtering step.
onlyActiveFilters	Logical scalar, whether to only include the active filters (i.e., where any read was filtered out in any of the samples). Defaults to TRUE.
displayNumbers	Logical scalar, indicating whether to display the number (or fraction) of reads retained at every filtering step.
numberSize	Numeric scalar, indicating the size of the displayed numbers (if displayNumbers is TRUE).
plotType	Character scalar, indicating what to show in the plot. Either "remaining" or "filtered".
facetBy	Character scalar, indicating the variable by which the plots should be facetted. Either "sample" or "step".

Details

The function assumes that the number of reads filtered out in each step are provided as columns of colData(se), with column names of the form f[0-9]_filteringreason, and that all filtering columns occur between the columns named nbrTotal and nbrRetained.

Value

A ggplot object.

Author(s)

Charlotte Soneson

Examples

se <- readRDS(system.file("extdata", "GSE102901_cis_se.rds", 
                          package = "mutscan"))[1:200, ]
plotFiltering(se)

fmicompbio/mutscan documentation built on March 30, 2024, 9:13 a.m.