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.
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
( |
| 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 |
| colorB | Optional R color for sample B. Defaults to |
A line plot of one or two samples, either on screen or as a .png file (in the working directory).
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.
# 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') # }