Visualize the filtering procedure

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".

Value

A ggplot object.

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.

Author

Charlotte Soneson

Examples

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