wiggle_plot: Wiggle data line plot
In hochwagenlab/hwglabr: Collection of R functions used in the Hochwagen Lab

wiggle_plot

R Documentation

Wiggle data line plot

Description

This function allows you to plot wiggle data for a selected chromosome. It takes as input either the raw wiggle data (for example one element of the 16 chromosome list) or the output of wiggle_smooth() (R data frame with two columns: genome position and smoothed signal).

Usage

wiggle_plot(wiggleData, chr, genome, yMax, color = "grey50", protein,
  legendXcoord = -10, legendYcoord = yMax,
  legendAnnotation = deparse(substitute(wiggleData)), onScreen = TRUE)

Arguments

`wiggleData`	A data frame of wiggle data with two columns: genome position and signal. No default.
`chr`	A number representing the chromosome of `wiggleData`. No default.
`genome`	A string representing the genome used for mapping. No default.
`yMax`	Optional number to be used as the max Y scale value in the plots. Particularly useful to plot two chromosomes on the same Y scale. No default.
`color`	Optional R color. Defaults to `grey50`.
`protein`	A string representing the ChIPped protein. No default.
`legendXcoord`	A number representing the X coordinate to locate legend. Defaults to minimum X (left-aligned).
`legendYcoord`	A number representing the Y coordinate to locate legend. Defaults to maximum Y (top-aligned).
`legendAnnotation`	Optional string to be used as the legend. Defaults to name of object passed to the function.
`onScreen`	Boolean indicating plots should be returned to the screen (`onScreen = TRUE`) or written to .png files (`onScreen = FALSE`). Defaults to `TRUE`.

Value

A line plot, either on screen or as a png file (in the working directory).

Examples

## Not run: 
wiggle_plot(WT[[1]], 1, genome = 'SK1', protein = 'Red1')

wiggle_plot(WT_chr3, 3, genome = 'SK1', yMax = 5, color = 'red', protein = 'Red1', onScreen = TRUE)

wiggle_plot(chrXVI, 16, genome = 'S288C', yMax = 5, color = 'black',
            protein = 'Rec8-HA', legendXcoord = 600, onScreen = FALSE)

## End(Not run)

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