signal_at_conv_average_plot: Line plot of average signal between convergent genes

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

Line plot of average signal between convergent genes

Description

Deprecated! Use signal_at_intergen_average_plot instead.
This function allows you to make a line plot of the ChIP signal over the average intergenic region centered on midpoints of convergent genes. It takes as input a data frame containing the average signal centered on the midpoints of convergent gene regions.

Usage

signal_at_conv_average_plot(inputDataA, inputDataB, genome, yMax,
  onScreen = TRUE, legendXcoord = xMin + xMin * 0.2, legendYcoord = yMax +
  yMax * 0.05, colorA = "grey50", colorB = "orange")

Arguments

inputDataA	A data frame of average signal between convergent genes: relative position and average signal. No default.
inputDataB	Optional data in the same format for a second sample. No default.
genome	A string representing the genome used for mapping. This is used in the title of the plot only. No default.
yMax	Optional number to be used as the max Y scale value in the plot.
onScreen	Boolean indicating plots should be returned to the screen (onScreen = TRUE) or written to .png files (onScreen = FALSE). Defaults to TRUE.
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).
colorA	Optional R color for sample A. Defaults to grey50.
colorB	Optional R color for sample B. Defaults to green.

Details

To generate the input for this function starting from an R list of wiggle data for the 16 chromosomes you should run: 1. signal_at_conv() to pull out the signal at every convergent gene region.

2. signal_average() to calculate the average signal over all regions.

Value

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

Examples

## Not run: 
signal_at_conv_average_plot(WT_conv_mean_signal, genome = 'S288C')

signal_at_conv_average_plot(WT_conv_mean_signal, dot1_conv_mean_signal, genome = 'SK1',
                            yMax = 3, onScreen = FALSE, legendXcoord = -500,
                            legendYcoord = 1, colorA = 'red', colorB = 'green')

## End(Not run)

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