This function allows you to make a line plot of the ChIP signal over the average ORF. It takes as input a data frame containing the average signal over ORFs (+/- flanking regions) genome-wide.
signal_at_orf_average_plot(inputDataA, inputDataB, genome, yMin, yMax, onScreen = TRUE, legendXcoord = -200, legendYcoord = yMax + yMax * 0.05, colorA = "grey50", colorB = "orange", smoothBandwidth = 0)
inputDataA | A data frame of average signal on ORFs +/- 1/2 the length of the ORF: relative position and average signal. No default. |
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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. |
yMin | Optional number to be used as the minimum Y scale value in the plot. |
yMax | Optional number to be used as the maximum 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 |
smoothBandwidth | Optional integer as the bandwith for smoothing data (for better-looking
line plots) using a Kernel Regression Smoother. Smoothing is performed using function
|
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:
signal_at_orf
to pull out the signal at every ORF and flanking regions
(1/2 the length of the ORF).
signal_average
to calculate the average signal at each relative position
over all regions genome-wide.
# NOT RUN { signal_at_orf_average_plot(WT_orf_S288C_mean_signal, genome = 'S288C') signal_at_orf_average_plot(WT_orf_mean_signal, dot1_orf_mean_signal, genome = 'SK1', yMax = 3, onScreen = FALSE, legendXcoord = -500, legendYcoord = 1, colorA = 'red', colorB = 'green', smoothBandwidth = 50) # }