plot_failed_mapping_count: Plot Salmon failed mapping count

In bryancquach/omixjutsu: Utilities for omics analysis tasks

Plot Salmon failed mapping count

Description

Create a Salmon failed mapping histogram and boxplot. The two plots are intended to be used as a single column, two row figure panel.

Usage

plot_failed_mapping_count(
  data,
  group = NULL,
  ids = NULL,
  invert = F,
  return_data = F,
  binsize = NULL,
  colors = NULL,
  hist_alpha = 0.75,
  box_fill = "goldenrod",
  box_alpha = 0.5,
  box_lwd = 1,
  jitter_alpha = 0.75,
  jitter_size = 1.75,
  x_title = paste0(c("Number of failed mappings", "for mapped fragments (millions)"),
    collapse = "\n"),
  y_title = "Sample count"
)

Arguments

data	A data frame with Salmon mapping data in the same format as salmon returned by load_paired_end_qc_data.
group	A single column data frame denoting categorical variable values to use to partition the data points into separate distributions/boxplots. Row names should match rownames in data.
ids	A vector of rownames for subsetting data for plotting.
invert	A logical. Should ids be used for excluding rows from plotting instead?
return_data	A logical. Should plot data be returned instead of a ggplot object?
binsize	A numeric value for the histogram bin widths.
colors	A string vector. The histogram bar colors and jitter colors for each categorical variable value.
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_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 ggplot object unless return_data is TRUE, then a data frame with the mean of mean PHRED scores and grouping variable.

A list with two ggplot objects hist and boxplot corresponding to a histogram and jittered boxplot respectively. If return_data is TRUE, then a data frame with the plot data values and grouping variable.

See Also

\link{load_paired_end_qc_data}

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