signal_at_conv_average_plot: Line plot of average signal between convergent genes
In luisvalesilva/hwglabr: Collection of R functions used in the Hochwagen Lab

Description Usage Arguments Details Value Examples

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.

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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")

`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`.

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.

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

## 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)