barplot_custom_histogram.R

#=============================================================================
## Template that uses base R to bin a variable in a custom manner and plot the
## frequency of the bins in a barplot (histogram). This template demonstrates
## adjusting the following plot features using base R:
## - Binning
## - Margin size
## - Line thickness
## - Plot colors
## - Axis title position, font size and content
## - Axis labels position, orientation, values, size
## - Text labels
## This example plots a variable whose values encode genomic distances for
## enhancer - gene pairs
#=============================================================================

# Adjust margins and line width
opar <- par(lwd = 3.5, mar = c(9, 7, 9, 2) + 0.1)

# distance is the variable of interest
distance <- abs(distance)

# Binning and frequency calculation
distance_binned <- .bincode(distance, c(7000,10000,50000,100000,200000,500000,1e+6,10e+6, 40e+6), include.lowest=T)
t <- table(distance_binned)

# Barplot (custom histogram) generation
x <- barplot(t, main="",
            col="#a6bddb", border="black",
            cex.axis=2, las=2, xaxt="n", ylim=c(0,6000));

# Axes titles
title(ylab="Frequency (Number of Enhancer - Gene Pairs)", line=5.5, cex.lab=2);
title(xlab="Enhancer - TSS distance", line=8, cex.lab=2);

# X axis labels adjustment
text(x = x+0.3, y = par("usr")[3] - 0.45,
    labels = c("7 - 10 kb", "10 - 50 kb", "50 - 100 kb", "100 - 200 kb", "200 - 500 kb", "0.5 - 1 Mb", "1 - 10 Mb", "10 - 40 Mb"),
    xpd = NA, srt = 35, cex = 2, adj = 1.2);

# Text label for each bar
text(x=x, y=t, labels=t, pos=3, xpd=NA, cex=2);