makePlot.genebody.coverage {QoRTs}R Documentation

Plot Gene-Body coverage distribution

Description

Plots Gene-Body coverage distribution

Usage

  makePlot.genebody(plotter, 
                  geneset = c("Overall","90-100","75-90","50-75","0-50"),
                  avgMethod = c("TotalCounts", "AvgPercentile"), 
                  plot.medians, 
                  plot.means = TRUE, 
                  debugMode, 
                  singleEndMode, 
                  rasterize.plotting.area = FALSE, raster.height = 1000, raster.width = 1000,
                  plot = TRUE,
                  ... )

  #NOTE: The preferred method to access the below functions
  #  is to use makeplot.genebody and set:
  #  avgMethod = "TotalCounts"
  #DEPRECIATED:
  makePlot.genebody.coverage(plotter, plot.medians,
                       plot.means = TRUE,  
                       debugMode, singleEndMode, 
                       rasterize.plotting.area = FALSE, raster.height = 1000, raster.width = 1000,
                       plot = TRUE,
                       ...)
  #DEPRECIATED:
  makePlot.genebody.coverage.UMQuartile(plotter, plot.medians, 
                       plot.means = TRUE, 
                       debugMode, singleEndMode, 
                       rasterize.plotting.area = FALSE, raster.height = 1000, raster.width = 1000,
                       plot = TRUE,
                       ...)
  #DEPRECIATED:
  makePlot.genebody.coverage.lowExpress(plotter, plot.medians, 
                       plot.means = TRUE, 
                       debugMode, singleEndMode,
                       rasterize.plotting.area = FALSE, raster.height = 1000, raster.width = 1000,
                       plot = TRUE,
                       ...)

Arguments

plotter

A QoRT_Plotter reference object. See build.plotter.

geneset

The set of genes to plot the gene-body coverage over. Genes are grouped into four quantiles by their by their total read counts: the 90-100 quantile, the 75-90 quantile, the 50-75 quantile (or "upper-middle quartile"), and the 0-50 quantile. By default it will plot the overall gene-body coverage across all genes.

avgMethod

The method used to generate average gene body coverage.

The "TotalCounts" (default) method simply takes the sum of each bin across all genes in the geneset, then for each replicate normalizes the coverage into frequencies.

The "AvgPercentile" calculates the coverage distribution across each percentile bin and normalizes the counts so they add up to 1, FOR EACH GENE, and THEN averages those values across all genes in the geneset.

The latter variant is experimental. the idea was for it to reduce the impact of highly-expressed genes and gain a better estimate of the degree of 5'/3' bias.

plot.medians

A logical value indicating whether or not to plot the median average for each bamfile at the bottom of the plot. Overrides plot.means.

plot.means

A logical value indicating whether or not to plot the mean average for each bamfile at the bottom of the plot.

debugMode

Logical. If TRUE, debugging data will be printed to the console.

singleEndMode

Logical. Determines whether the dataset consists of single-ended reads. By default this is determined from the data. Thus, this parameter should never need to be set by the user.

rasterize.plotting.area

Logical. If TRUE, then "flatten" the plotting lines into a raster format. This requires support for png file creation and the installation of the "png" package. Only the plotting lines will be rasterized, the axes and annotations will be vector format. Default is FALSE.

raster.height

Numeric integer. If rasterize.plotting.area is TRUE, then this will set the height of the rasterized plot, in pixels.

raster.width

Numeric integer. If rasterize.plotting.area is TRUE, then this will set the width of the rasterized plot, in pixels.

plot

Logical. If FALSE, suppress plotting and return TRUE if and only if the data is present in the dataset to allow plotting. Useful to automatically filter out missing data plots.

...

Arguments to be passed to methods, such as graphical parameters (see par).

Details

x-axis: Gene-body quantile. By default this is broken up into 40 quantiles containing 2.5

y-axis: Rate at which reads falls into the given quantile of the genes' bodies.

makePlot.genebody.coverage plots the gene body coverage across all genes. makePlot.genebody.coverage.UMQuartile plots the gene body coverage across the genes that fall in the upper-middle quartile of total expression for each sample-run (excluding genes with zero reads). makePlot.genebody.coverage.lowExpress plots the gene body coverage across the genes that fall in the lower two quartiles of total expression for each sample-run (excluding genes with zero reads).

See Also

build.plotter

Examples

  data(res,package="QoRTsExampleData");
  plotter <- build.plotter.colorByGroup(res);
  makePlot.genebody(plotter, geneset = "Overall");

## Starting: Gene-Body Coverage plot.

## Finished: Gene-Body Coverage plot.[time: 2018-09-25 13:12:34],[elapsed: 0.13 secs]

plot of chunk unnamed-chunk-1

  makePlot.genebody(plotter, geneset = "90-100");

## Starting: Gene-Body Coverage, Top 10 Percentile Genes plot.

## Finished: Gene-Body Coverage, Top 10 Percentile Genes plot.[time: 2018-09-25 13:12:34],[elapsed: 0.18 secs]

plot of chunk unnamed-chunk-1

  makePlot.genebody(plotter, geneset = "50-75");

## Starting: Gene-Body Coverage, Upper Middle Quartile Genes plot.

## Finished: Gene-Body Coverage, Upper Middle Quartile Genes plot.[time: 2018-09-25 13:12:35],[elapsed: 0.18 secs]

plot of chunk unnamed-chunk-1

[Package QoRTs version 1.3.6 Index]