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

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.

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.

Author(s)

Paul Pyl

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(h5vc)
Loading required package: grid
Loading required package: gridExtra
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/h5vc/geom_h5vc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geom_h5vc
> ### Title: geom_h5vc
> ### Aliases: geom_h5vc
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>