signal_at_intergen_average_plot: Line plot of average signal on intergenic regions
In luisvalesilva/hwglabr: Collection of R functions used in the Hochwagen Lab

Description Usage Arguments Details Value Examples

This function allows you to make a line plot of the average ChIP signal on specific intergenic regions. It takes as input a data frame containing the average signal in a window of positions centered on the midpoints of a specified type of intergenic region.

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signal_at_intergen_average_plot(inputDataA, inputDataB, genome, orientation,
  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.
`orientation`	A string representing the type of intergenic region (convergent, divergent or tandem). 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:

signal_at_intergen to pull out the signal at every intergenic region.
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_intergen_average_plot(WT_conv_mean_signal, genome = 'S288C', orientation = 'Convergent')

signal_at_intergen_average_plot(WT_div_mean_signal, dot1_conv_mean_signal, genome = 'SK1',
                                orientation = 'Div', yMax = 3, onScreen = FALSE,
                                legendXcoord = -500, legendYcoord = 1,
                                colorA = 'red', colorB = 'green')

## End(Not run)