plot_hisat2_mapping_rate: Plot HISAT2 mapping percentage

In bryancquach/omixjutsu: Utilities for omics analysis tasks

Plot HISAT2 mapping percentage

Description

Create a HISAT2 concordant alignment rate histogram and boxplot. The two plots are intended to be used as a single column, two row figure panel. Only applicable for paired-end sequencing data.

Usage

plot_hisat2_mapping_rate(
  data,
  ids = NULL,
  invert = F,
  binsize = NULL,
  hist_fill = "gray10",
  hist_alpha = 0.75,
  box_fill = "goldenrod",
  box_alpha = 0.5,
  box_lwd = 1,
  jitter_color = "gray30",
  jitter_alpha = 0.75,
  jitter_size = 1.75,
  x_title = "Concordant alignment rate",
  y_title = "Sample count"
)

Arguments

data	A data frame with HISAT2 mapping data in the same format as hisat2 returned by load_paired_end_qc_data.
ids	A vector of rownames for subsetting data for plotting.
invert	A logical. Should ids be used for excluding rows from plotting instead?
binsize	A numeric value for the histogram bin widths.
hist_fill	A string. The fill color for histogram bars.
hist_alpha	A numeric value for the alpha level for histogram bars.
box_fill	A string. The fill color for the boxplot.
box_alpha	A numeric value for the alpha level for the boxplot.
box_lwd	A numeric value for the boxplot line width.
jitter_color	A string. The point color for jittered data points.
jitter_alpha	A numeric for the alpha level for jittered data points.
jitter_size	A numeric for the point size for jittered data points.
x_title	A string denoting the x-axis title. Only added to the boxplot.
y_title	A string denoting the y-axis title. Only added to the histogram.

Value

A list with two ggplot objects hist and boxplot corresponding to a histogram and jittered boxplot respectively.

See Also

load_paired_end_qc_data

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