plotfeatureCoverage: Plot feature coverage results
In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description Usage Arguments Value Author(s) See Also Examples

Plots the 3 tabular data types (A-C) generated by the featureCoverage function. It accepts data from single or many features (e.g. CDSs) and samples (BAM files). The coverage from multiple features will be summarized using methods such as mean, while the data from multiple samples will be plotted in separate panels.

1	plotfeatureCoverage(covMA, method = mean, scales = "fixed", extendylim=2, scale_count_val = 10^6)

`covMA`	Object of class `data.frame` generated by `featureCoverage` function.
`method`	Defines the summary statistics to use when `covMA` contains coverage data from multiple features (e.g. transcripts). The default calculates the mean coverage for each positon and/or bin of the corresponding coverage vectors.
`scales`	Scales setting passed on to the `facet_wrap` function of `ggplot2`. For details see `ggplot2::facet_wrap`. The default `fixed` assures a constant scale across all bar plot panels, while `free` uses the optimum scale within each bar plot panel. To evaluate plots in all their details, it may be necessary to generate two graphics files one for each scaling option.
`extendylim`	Allows to extend the upper limit of the y axis when `scales=fixed`. Internally, the function identifies the maximum value in the data and then multiplies this maximum value by the value provided under `extendylim`. The default is set to `extendylim=2`.
`scale_count_val`	Scales (normalizes) the read counts to a fixed value of aligned reads in each sample such as counts per million aligned reads (default is 10^6). For this calculation the `N_total_aligned` values are used that are reported in the input `data.frame` generated by the upstream `featureCoverage` function. Assign `NULL` to turn off scaling.

Currently, the function returns ggplot2 bar plot graphics.

Thomas Girke

featureCoverage

## Construct SYSargs object from param and targets files 
param <- system.file("extdata", "tophat.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)

## Not run: 
## Features from sample data of systemPipeRdata package
library(GenomicFeatures)
file <- system.file("extdata/annotation", "tair10.gff", package="systemPipeRdata")
txdb <- makeTxDbFromGFF(file=file, format="gff3", organism="Arabidopsis")

## (A) Generate binned coverage for two BAM files and 4 transcripts
grl <- cdsBy(txdb, "tx", use.names=TRUE)
fcov <- featureCoverage(bfl=BamFileList(outpaths(args)[1:2]), grl=grl[1:4], resizereads=NULL, 
                    readlengthrange=NULL, Nbins=20, method=mean, fixedmatrix=FALSE, 
                    resizefeatures=TRUE, upstream=20, downstream=20)
fcov <- featureCoverage(bfl=BamFileList(outpaths(args)[1:2]), grl=grl[1:4], resizereads=NULL, 
                    readlengthrange=NULL, Nbins=20, method=mean, fixedmatrix=TRUE, 
                    resizefeatures=TRUE, upstream=20, downstream=20)
plotfeatureCoverage(covMA=fcov, method=mean, scales="fixed", scale_count_val=10^6)

## (B) Coverage matrix upstream and downstream of start/stop codons
fcov <- featureCoverage(bfl=BamFileList(outpaths(args)[1:2]), grl=grl[1:4], resizereads=NULL, 
                    readlengthrange=NULL, Nbins=NULL, method=mean, fixedmatrix=TRUE, 
                    resizefeatures=TRUE, upstream=20, downstream=20)
plotfeatureCoverage(covMA=fcov, method=mean, scales="fixed", scale_count_val=10^6)

## (C) Combined matrix for both binned and start/stop codon 
fcov <- featureCoverage(bfl=BamFileList(outpaths(args)[1:2]), grl=grl[1:4], resizereads=NULL, 
                    readlengthrange=NULL, Nbins=20, method=mean, fixedmatrix=TRUE, 
                    resizefeatures=TRUE, upstream=20, downstream=20, outfile="results/test.xls")
plotfeatureCoverage(covMA=fcov, method=mean, scales="fixed", scale_count_val=10^6)

## (D) Rle coverage objects one for each query feature
fcov <- featureCoverage(bfl=BamFileList(outpaths(args)[1:2]), grl=grl[1:4], resizereads=NULL, 
                    readlengthrange=NULL, Nbins=NULL, method=mean, fixedmatrix=FALSE, 
                    resizefeatures=TRUE, upstream=20, downstream=20)


## End(Not run)