set_summary_parameters: set_summary_parameters

In skummerf/GenomicWidgets: interactive visualization of genomics data

Description

Setup parameters for plotting summaries along genome tracks. Result from this function can be passed to set_track_parameters

Usage

## S4 method for signature 'SummarizedExperiment'
set_summary_parameters(object, ranges,
  assay_name = assayNames(object)[1], groups = colnames(object),
  colors = "blue", showlegend = length(colors) > 1, boxpoints = c("all",
  "Outliers", "false"), pointpos = 0, ytitle = "Expression", width = 0.3)

## S4 method for signature 'RangedSummarizedExperiment'
set_summary_parameters(object,
  ranges = rowRanges(object), assay_name = assayNames(object)[1],
  groups = NULL, colors = "blue", showlegend = length(colors) > 1,
  boxpoints = c("all", "Outliers", "false"), pointpos = 0,
  ytitle = "Expression", width = 0.3)

Arguments

object	SummarizedExperiment
ranges	ranges corresponding to rows of object
assay_name	name of assay to use
groups	either vector of group assignments of name of column in object colData that corresponds to vector of group assignments
colors	colors to use
showlegend	show the legend?
boxpoints	plot individual points?
pointpos	relative position of points to boxes
ytitle	name for yaxis
width	relative width of summary plots when plotting tracks
...	additional arguments

Value

object storing summary parameters, for use in set_track_parameters

Author(s)

Alicia Schep and Justin Finkle

Examples

library(GenomicRanges)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

## we'll read in some RNA counts
data(rpkm_chr21)

## From the ranges of the rpkm object, we'll pull out the tss
chr21_promoters <- promoters(SummarizedExperiment::rowRanges(rpkm_chr21),
                 up = 1000, down = 1000)

## set summary parameters

summary_params <- set_summary_parameters(rpkm_chr21,
  groups = "GROUP", ranges = chr21_promoters) 
  
## We'll also read in some track data to plot
genomation_dir <- system.file("extdata", package = "genomationData")
samp.file <- file.path(genomation_dir,'SamplesInfo.txt')
samp.info <- read.table(samp.file, header=TRUE, sep="\t", 
                        stringsAsFactors = FALSE)
samp.info$fileName <- file.path(genomation_dir, samp.info$fileName)

## Make track plotter using summary parametrs

track_params <- set_track_parameters(samp.info$fileName[1:3], 
  annotation = TxDb.Hsapiens.UCSC.hg19.knownGene, 
  track_names = samp.info$sampleName[1:3], 
  share_y = TRUE,
  summary = summary_params)
  
if (interactive()){
  plot_tracks(rownames(rpkm_chr21)[1:3], track_params)
  plot(chr21_promoters[1:3], track_params)
}   

skummerf/GenomicWidgets documentation built on May 31, 2019, 6:16 p.m.