plotReadStats {icetea} | R Documentation

## Plot read statistics from the CapSet object

### Description

Plot read statistics from the CapSet object

### Usage

    plotReadStats(
      CSobject,
      plotType = "dodge",
      plotValue = "numbers",
      outFile = NULL
    )

    ## S4 method for signature 'CapSet'
    plotReadStats(
      CSobject,
      plotType = "dodge",
      plotValue = "numbers",
      outFile = NULL
    )

### Arguments

`CSobject` | The `CapSet` object
`plotType` | character. The type of plot to make. Choose from "stack" or "dodge" for either a stacked barchart, or a bar chart with "dodged" positions (analogous to ggplot)
`plotValue` | character. What values to plot. Choose from "numbers" or "proportions". If "proportions" is selected, the proportion of reads w.r.t total demultiplexed reads per sample would be plotted
`outFile` | character. Output file name. (filename extention would be used to determine type). If outfile not specified, the plot would be retured on the screen

### Value

A ggplot object, or a file. Plot showing the number/proportion of reads in each category, per sample

### Examples

    # load a previously saved CapSet object
    cs <- exampleCSobject()
    plotReadStats(cs, plotType = "dodge", plotValue = "numbers", outFile = "test_numbers.pdf")

[Package icetea version 1.8.0 Index]