aspi (version 0.2.0)

plotVolcano: Volcano plot

Description

Produces scatterplot of statistical significance vs fold difference in parasite abundance between left and right.

Usage

plotVolcano(x, test = "G", pAdj = "BH", sigThresh = 0.05, ...)

Arguments

x

a matrix or data frame with two numeric columns; first column is for left-side and 2nd column for right-side. Identifiers for hosts can be provided as row names.

test

if set to "G" (default) a G-test is performed; otherwise an exact binomial test is performed.

pAdj

method for correcting p-values for multiple comparisons. If set to "BH" (default), Benjamini & Hochberg's procedure is used to control the false discovery rate (FDR); otherwise Holm's methos is used to control the familywise error rate (FWER).

sigThresh

significance threshold (defaults to 0.05); p-values below this value will be called significant.

...

optional further arguments and graphical parameters passed to plot.

Details

plot.Volcano creates a volcano plot, i.e. a scatterplot of statistical significance (-log10(p-value)) vs fold difference (log2 ratio - as calculated for the histogram above) in parasite abundance between left and right. Each point in the scatterplot represents the parasite distribution in an individual host. A dashed horizontal line represents the user-defined p-value threshold for significance. If a parasite distribution deviates significantly from symmetry it is shown as a red square, otherwise as a blue circle.

Examples

plotVolcano(diplostomum_eyes_excl_lenses)
plotVolcano(diplostomum_eyes_excl_lenses, test="G", pAdj="BH", sigThresh=0.1,
main="Diplostomum metacercariae in eyes of ruffe")