plotReadStats: Plot read statistics from the CapSet object
In icetea: Integrating Cap Enrichment with Transcript Expression Analysis

Description Usage Arguments Value Examples

Plot read statistics from the CapSet object

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

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

`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

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

1
2
3

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