chr_coverage_plot: Average chromosome signal (coverage) dot plot

In hochwagenlab/hwglabr: Collection of R functions used in the Hochwagen Lab

Average chromosome signal (coverage) dot plot

Description

This function allows you to plot average chromosome signal for one or two selected samples. It takes as input the output of chr_coverage (16x2 R data frame).

Usage

chr_coverage_plot(coverageDataA, coverageDataB, genome, meanNorm = FALSE,
  yMax, onScreen = TRUE, fileName, colorA = "grey50", colorB = "green")

Arguments

coverageDataA	A 16x2 data frame of coverage: chromosome and average signal. No default.
coverageDataB	Optional 16x2 data frame of coverage: chromosome and average signal. No default.
genome	A string representing the genome used for mapping. No default.
meanNorm	Boolean indicating whether input data are normalized to genome-wide averages (meanNorm = TRUE). If so, a line is added at y = 1. Defaults to FALSE.
yMax	Optional number to be used as the max Y scale value in the plots. No default.
onScreen	Boolean indicating plots should be returned to the screen (onScreen = TRUE) or written to .pdf files (onScreen = FALSE). Defaults to TRUE.
fileName	A string to name the output .pdf file in case (onScreen = FALSE). No default.
colorA	Optional R color for sample A. Defaults to grey50.
colorB	Optional R color for sample B. Defaults to green.

Value

A dot plot of one or two samples, either on screen or as a .pdf file (in the working directory).

Examples

## Not run: 
chr_coverage_plot(WT, rec8, genome = 'SK1', onScreen = TRUE, colorB = 'red')

chr_coverage_plot(WT, dot1, genome = 'S288C', meanNorm = TRUE,
                  onScreen = FALSE, fileName='chr_coverage_WT_and_dot1.pdf')

## End(Not run)

hochwagenlab/hwglabr documentation built on Feb. 25, 2025, 5:41 a.m.