View source: R/plotFiltering.R
plotFiltering | R Documentation |
Display the number (or fraction) of reads remaining after each step
of the internal mutscan
filtering.
plotFiltering(
se,
valueType = "reads",
onlyActiveFilters = TRUE,
displayNumbers = TRUE,
numberSize = 4,
plotType = "remaining",
facetBy = "sample"
)
se |
A |
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 |
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 |
plotType |
Character scalar, indicating what to show in the plot.
Either |
facetBy |
Character scalar, indicating the variable by which the plots
should be facetted. Either |
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
.
A ggplot
object.
Charlotte Soneson
se <- readRDS(system.file("extdata", "GSE102901_cis_se.rds",
package = "mutscan"))[1:200, ]
plotFiltering(se)
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