plotReadCountDistributions: Plot bar chart of read counts or cumulative read KB in bins

In mgaleyuw/NanoGraph: Export Graphs and Statistics from Nanopore Metadata

Description

Uses metadata DataFrame to plot the distribution of reads in ggplot. Can plot read quality in stacked bars, manipulate the width of bins.

Usage

plotReadCountDistributions(
  indf,
  outname,
  binNum = 50,
  counts = FALSE,
  skinnyBin = FALSE,
  outwidth = 8,
  outheight = 7,
  outunits = "in",
  plotQual = FALSE,
  qual.bins = c(10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60),
  barColor = "#8ec462",
  indf2 = NA,
  barColorRamp = c("#8ec462", "firebrick1"),
  dodgeAdjust = 10000,
  sampleNames = c("Sample 1", "Sample 2"),
  binWidth = NA
)

Arguments

indf	DataFrame of read metadata
outname	Filename for plot to save. Can be .pdf or .png. Set to NA to skip plot saving.
binNum	Number of Bins
counts	TRUE or FALSE, default FALSE, plot counts, not cumulative KB
skinnyBin	TRUE or FALSE, default FALSE, make bars skinny for overlay
outwidth	width dimension to save plot
outheight	height dimension to save plot
outunits	unit of width and height, default 'in'
plotQual	TRUE or FALSE, default FALSE, plot quality distribution as fill
qual.bins	a vector of quality cutoffs for use with plotQual
barColor	an r color or color hex code
indf2	DataFrame of read metadata for a second sample
dodgeAdjust	a number to adjust the spacing of color mapped bars. Default is 10kb.
sampleNames	a vector of samplenames for plotting two datasets
binWidth	a number, representing width of bins. overrides skinnybin.
colorMapVar	name of a column in df to map fill to

Value

a ggplot2 plot

mgaleyuw/NanoGraph documentation built on Dec. 21, 2021, 5:08 p.m.