plotCIs {Rariant} | R Documentation |
The 'plotConfidenceIntervals' is a high-level plotting function for visualizing confidence intervals. The 'plotAbundanceShift' function visualizes the shift in mismatch rates between two samples.
plotConfidenceIntervals(x, ylim = c(-1.05, 1.05), color = NULL, ...) plotAbundanceShift(x, ylim = c(-0.05, 1.05), rates = TRUE, ...)
x |
'GRanges' with mcols of a CI method, or 'data.frame' as returned by one of the CI methods, with the optional column 'start'. |
ylim |
Limits of the y-axis. Using this instead of using the 'ylim' prevents ugly warnings of 'ggplot2'. |
color |
Variable that determines the coloring of the confidence axis (character). |
rates |
Should the non-consensus rates of both samples be visualized as colored end points of the line range? (logical, default: TRUE). |
... |
Additional plotting arguments that are passed on to ggplot2::geom_pointrange. |
For a 'GRanges' input: A 'ggbio' object
For a 'data.frame' input: A 'ggplot' object
## Generate sample data counts = data.frame(x1 = 1:5, n1 = 30, x2 = 0:4, n2 = 30) ## Agresti-Caffo ci_ac = with(counts, acCi(x1, n1, x2, n2)) library(GenomicRanges) gr = GRanges("1", IRanges(start = 1:nrow(counts), width = 1)) mcols(gr) = ci_ac ## GRanges plotConfidenceIntervals(gr) ## data.frame plotConfidenceIntervals(ci_ac) ## abundance shift plotAbundanceShift(gr) plotAbundanceShift(ci_ac)