plot_salmon_categories: Plot Salmon mapping category percentages

In bryancquach/omixjutsu: Utilities for omics analysis tasks

Plot Salmon mapping category percentages

Description

Create barplots with percentages for types of Salmon mappings.

Usage

plot_salmon_categories(
  data,
  fill = brewer.pal(n = 4, name = "Spectral"),
  sort = F,
  ids = NULL,
  invert = F
)

Arguments

data	A data frame with Salmon mapping data in the same format as salmon returned by load_paired_end_qc_data.
fill	A string vector with 4 colors corresponding to bars for the barplots for the transcriptome, decoys, dovetails, and filtered mappings respectively.
sort	A logical. Should the x-axis be ordered by transcriptome mapping rate?
ids	A vector of rownames for subsetting data for plotting.
invert	A logical. Should ids be used for excluding rows from plotting instead?

Details

Create barplots with the percentage of reads/read pairs input into Salmon that were mapped to the transcriptome, decoy fragments, as dovetails, and as low-score filtered mappings. Categories are not mutually exclusive. X-axes are ordered the same across plots.

Value

A list with four ggplot objects transcriptome, decoy, dovetail, and filtered that correspond to the plots for the transcriptome, decoys, dovetails, and filtered mappings respectively.

See Also

load_paired_end_qc_data

bryancquach/omixjutsu documentation built on Jan. 29, 2023, 3:47 p.m.