ct.signalSummary: Generate a Figure Summarizing Overall Signal for One or More...

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

Generate a Figure Summarizing Overall Signal for One or More Targets

Description

Given one or more targets of interest, this function generates a summary image contextualizing the corresponding signals within the provided contrast. This takes the form of an annotated ranking curve of target-level signals, supplemented with horizontal Q-value cutoffs and an inset volcano plot of gRNA behavior.

Limited annotation is provided for the specified targets using the following logic:

- If a character vector is provided, up to five targets are annotated; longer lists are highlighted without specifying individual elements. - If a list is provided, the 'names' element is used as the annotation. This is similarly constrained to a total of 5 annotated elements.

Usage

ct.signalSummary(summaryDF, targets, callout = FALSE, ...)

Arguments

summaryDF	A dataframe summarizing the results of the screen, returned by the function ct.generateResults.
targets	A list or character vector containing the names of the targets to be displayed. Only targets contained in the column specified by the 'collapse' parameter to 'ct.simpleResult()' will be displayed; default is 'geneSymbol'. Plotting priority (e.g., the points to plot last in the case of overlapping signals) is given to earlier elements in the list.
callout	Logical indicating whether lines should be plotted indicating individual gene sets to augment the point highlighting.
...	Additional optional arguments to 'ct.simpleResult()'

Value

A summary plot on the current device.

Author(s)

Russell Bainer

Examples

data('resultsDF')
ct.signalSummary(resultsDF, list('CandidateA' = 'Target229', 'Pathway3' = resultsDF$geneSymbol[c(42,116,1138,5508)]))

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