ct.contrastBarchart: Visualize Signal Across A List of Contrasts

In OscarBrock/gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Visualize Signal Across A List of Contrasts

Description

Given a list of provided results 'data.frame's summarizing a series of contrasts from one or more pooled screens, this function visualizes their respective signals as a series of stacked barcharts. Enriched signals are represented in the positive direction, and depleted signals are represented in the negative direction. Note that the provided contrast results are not regularized by this function.

This function may be used to compare signals across different screen contrasts, or to compare signals within interesting subsets of targets ascertained within a single experiment.

Usage

ct.contrastBarchart(
  dflist,
  background = TRUE,
  statistic = c("best.q", "best.p"),
  ...
)

Arguments

dflist	A named list of 'data.frame's summarizing the results of one or more screen contrasts, returned by the function ct.generateResults.
background	Logical indicating whether to represent the nonsignificant hits in the barchart.
statistic	Should cutoffs be calculated based on FDR ('best.q') or P-value ('best.p')?
...	Other parameters to lower functions, especially 'ct.simpleResult()'

Value

A summary plot on the current device. Invisibly, the data.frame tallying signals at various thresholds.

Author(s)

Russell Bainer

Examples

data('resultsDF')
ct.contrastBarchart(list('FirstResult' = resultsDF, 'SecondResult' = resultsDF))
ct.contrastBarchart(list('FirstResult' = resultsDF, 'SecondResult' = resultsDF), background = FALSE)
ct.contrastBarchart(list('FirstResult' = resultsDF[1:1000,], 'SecondResult' = resultsDF))

OscarBrock/gCrisprTools documentation built on Oct. 25, 2022, 7:29 a.m.