rliger (version 2.2.1)

plotBarcodeRank: Create barcode-rank plot for each dataset

Description

This function ranks the total count of each cell within each dataset and make line plot. This function is simply for examining the input raw count data and does not infer any recommended cutoff for removing non-cell barcodes.

Usage

plotBarcodeRank(object, ...)

Value

A list object of ggplot for each dataset

Arguments

object

A liger object.

...

Arguments passed on to .ggScatter, .ggplotLigerTheme

dotSize,dotAlpha

Numeric, controls the size or transparency of all dots. Default getOption("ligerDotSize") (1) and 0.9.

raster

Logical, whether to rasterize the plot. Default NULL automatically rasterize the plot when number of total dots to be plotted exceeds 100,000.

title,subtitle,xlab,ylab

Main title, subtitle or X/Y axis title text. By default, no main title or subtitle will be set, and X/Y axis title will be the names of variables used for plotting. Use NULL to hide elements. TRUE for xlab or ylab shows default values.

baseSize

One-parameter control of all text sizes. Individual text element sizes can be controlled by other size arguments. "Title" sizes are 2 points larger than "text" sizes when being controlled by this.

panelBorder

Whether to show rectangle border of the panel instead of using ggplot classic bottom and left axis lines. Default FALSE.

plotly

Whether to use plotly to enable web based interactive browsing for the plot. Requires installation of package "plotly". Default FALSE.

Examples

plotBarcodeRank(pbmc)