plot_cumfrac_rpc: Plot cumulative fraction of reads per cell barcode

In argschwind/dropseqr: Utilities for Drop-seq data processing

Description

Calculate and plot cumulative fraction of reads per detected cell barcode. The cumulative fraction can be plotted to estimate the number of sequenced cells by identifying the "knee" of the distribution. For further details on selection of cells, see the Drop-seq alignment cookbook provided by the McCarroll lab.

Usage

plot_cumfrac_rpc(read_counts, nbcs = 50000, title = NULL, size = 1,
  cumfrac_col = "steelblue", ncells = NULL, ncells_col = "red")

Arguments

read_counts	A data.frame containing the number of reads per cell barcode. Should consist of two columns, whereas the number of reads must in the first and the barcode identity in the second column. This is typically produced by running BAMTagHistogram from Drop-seq tools.
nbcs	Number of cell barcodes to be plotted on the x-axis.
title	String containing plot title.
size	Size used for plotting the cumulative fraction and optional ncell line.
cumfrac_col	Color for plotting the cumulative fraction line
ncells	(optional) Estimate of how many cells are inculed in sample. A vertical line will be drawn at x = ncells.
ncells_col	Color for plotting the vertical line if ncells is specified.

Examples

library(dropseqr)

# load example dataset
data(reads_per_cell_barcode)

# cumulative fraction with default settings
plot_cumfrac_rpc(reads_per_cell_barcode, title = "Experiment 42")

# zoom in and draw line at estimated number of cells
plot_cumfrac_rpc(reads_per_cell_barcode, title = "Experiment 42",
              nbcs = 30000, ncells = 3500)

argschwind/dropseqr documentation built on May 23, 2019, 4:24 p.m.