h5vc (version 2.6.3)

geom_h5vc: geom_h5vc

Description

Plotting function that returns a ggplot2 layer representing the specified dataset for the specified samples in the region [positon - windowsize, position + windowsize].

Usage

geom_h5vc( data, sampledata, samples=sampledata$Sample, windowsize, position, dataset, ... )

Arguments

data

The data to be plotted. Returned by h5dapply. Must be centered on position, extend by windowsize in each direction and contain a slot named like the dataset argument

sampledata

The sampledata for the cohort represented by data. Returned by getSampleData

samples

A character vector listing the names of samples to be plotted, defaults to all samples as described in sampledata

windowsize

Size of the window in which to plot on each side. The total interval that is plotted will be [position-windowsize,position+windowsize]

position

The position at which the plot shall be centered

dataset

The slot in the data argument that should be plotted

...

Paramteters to be passed to the internally used geom_rect, see geom_rect for details

Value

• A ggplot layer object containing the plot of the specified dataset, this can be used like any other ggplot layer, i.e. it may be added to another plot.

Details

Creates a ggplot layer centered on position using the specified dataset from list data, annotating it with sample information provided in the data.frame sampledata and showing all samples listed in sample. The resulting plot uses ggplot2's geom_rect to draw boxes representing the values from dataset. The x-axis is the position and will span the interval [positon - windowsize, position + windowsize]. The x-axis is centered at 0 and additional layers to be added to the plot should be centered at 0 also. Ths function allows for fast creation of overview plots similar to mismatchPlot (without the stacking of tracks). The example below shows how one can create a plot showing the coverage and number of mismatches per position (but not the alternative allele) for a given region.

Examples

# loading library and example data
  library(h5vc)
  library(ggplot2)
  tallyFile <- system.file( "extdata", "example.tally.hfs5", package = "h5vcData" )
  sampleData <- getSampleData( tallyFile, "/ExampleStudy/16" )
  position <- 29979629
  windowsize <- 30
  samples <- sampleData$Sample[sampleData$Patient == "Patient8"]
  data <- h5dapply(
    filename = tallyFile,
    group = "/ExampleStudy/16",
    blocksize = windowsize * 3, #choose blocksize larger than range so that all needed data is collected as one block
    names = c("Coverages", "Counts", "Deletions"),
    range = c(position - windowsize, position + windowsize)
  )[[1]]
  # Summing up all mismatches irrespective of the alternative allele
  data$CountsAggregate = colSums(data$Counts)
  # Simple overview plot showing number of mismatches per position
  p <- ggplot() + 
  geom_h5vc( data=data, sampledata=sampleData, windowsize = 35, position = 500, dataset = "Coverages", fill = "gray" ) + 
  geom_h5vc( data=data, sampledata=sampleData, windowsize = 35, position = 500, dataset = "CountsAggregate", fill = "#D50000" ) + 
  facet_wrap( ~ Sample, ncol = 2 )
  print(p)