PeakError {PeakError} | R Documentation |
Compute true and false positive peak calls, with respect to a database of annotated regions.
PeakError(peaks, regions)
peaks |
data.frame with columns chrom, chromStart, chromEnd. NOTE: chromStart should be 0-based and chromEnd should be 1-based. EXAMPLE: the first 100 base of of a chromosome are chromStart=0, chromEnd=100. The second 100 bases are chromStart=100, chromEnd=200. |
regions |
data.frame with columns chrom, chromStart, chromEnd, annotation. |
data.frame for each region with additional counts of true positives (tp, possible.tp), false positives (fp, possible.fp, fp.status), and false negatives (fn, fn.status).
Toby Dylan Hocking
x <- seq(5, 85, by=5) peaks <- rbind(Peaks("chr2", x, x+3), Peaks("chr3", c(25, 38, 57), c(33, 54, 75)), Peaks("chr4", c(5, 32, 38, 65), c(15, 35, 55, 85)), Peaks("chr5", c(12, 26, 56, 75), c(16, 54, 59, 85))) regions <- NULL for(chr in 1:5){ regions <- rbind(regions, { data.frame(chrom=paste0("chr", chr), chromStart=c(10, 30, 50, 70), chromEnd=c(20, 40, 60, 80), annotation=c("noPeaks", "peakStart", "peakEnd", "peaks")) }) } err <- PeakError(peaks, regions) ann.colors <- c(noPeaks="#f6f4bf", peakStart="#ffafaf", peakEnd="#ff4c4c", peaks="#a445ee") library(ggplot2) ggplot()+ geom_rect(aes(xmin=chromStart+1/2, xmax=chromEnd+1/2, ymin=-1, ymax=1, fill=annotation, linetype=fn.status, size=fp.status), data=err, color="black")+ scale_y_continuous("", breaks=NULL)+ scale_linetype_manual(values=c("false negative"="dotted", correct="solid"))+ scale_size_manual(values=c("false positive"=3, correct=1))+ scale_fill_manual(values=ann.colors, breaks=names(ann.colors))+ facet_grid(chrom ~ .)+ theme_bw()+ guides(fill=guide_legend(order=1), linetype=guide_legend(order=2, override.aes=list(fill="white")), size=guide_legend(order=3, override.aes=list(fill="white")))+ theme(panel.margin=grid::unit(0, "cm"))+ geom_segment(aes(chromStart+1/2, 1/2, xend=chromEnd+1/2, yend=1/2), data=peaks, color="deepskyblue", size=2)+ scale_x_continuous("position on chromosome", breaks=seq(10, 90, by=10))+ geom_text(aes(base, -1/2, label="N"), data.frame(base=10:90), color="deepskyblue")