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

Description Usage Arguments Value Author(s) Examples

View source: R/GenerateSignalSummary.R

Description

Given one or more targets of interest, this function generates a summary image contextualizing the corresponding signals within the contest of 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

1
2
3
4
5
6
ct.signalSummary(
  summaryDF,
  targets,
  direction = c("enrich", "deplete"),
  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 geneSymbol column of the provided summaryDF are considered. Plotting priority (e.g., the points to plot last in the case of overlapping signals) is given to earlier elements in the list.

direction

Should enrichment or depletion be considered? Must be one of "enrich" or "deplete".

callout

Logical indicating whether lines should be plotted indicating individual gene sets to augment the point highlighting.

Value

A summary plot on the current device.

Author(s)

Russell Bainer

Examples

1
2
3
4
5
6
7
8
data('resultsDF')
ct.signalSummary(resultsDF, list('CandidateA' = 'Target229', 'Pathway3' = resultsDF$geneSymbol[c(42,116,1138,5508)]), 'enrich')
data('es')
data('ann')
data('fit')

ct.GCbias(es, ann)
ct.GCbias(fit, ann)

gCrisprTools documentation built on Nov. 8, 2020, 8:17 p.m.