repl.hs.comp: Replicate hotspot comparison

Description Usage Arguments Value Author(s) See Also Examples

View source: R/repl.hs.comp.R

Description

This function calculates hotspot correlation, loss, gain or balance for the different replicates per sampling scheme and taxonomic group.

Usage

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repl.hs.comp(seqsubmats.hs, hs.baseline, method = "Phi", 
stats = TRUE, plot = TRUE, plot.mean = TRUE, ylim = NULL, 
horiz.line = NA)

Arguments

seqsubmats.hs

hotspots for the seqsubmats

hs.baseline

hotspots for the baseline

method

binary comparison method to use. See binary.comparison for available options.

stats

logical, whether to calculate also the stats (mean, min, max, sd) of the replicate comparison for each group.

plot

logical, whether to plot the hotspot comparison values per replicate per group.

plot.mean

logical, whether to plot (with a white circle) the mean value of the replicates per group.

ylim

limits for the y axis. The default is NULL for automatic limits, but you may want to use ylim = c(0,1) for e.g. phi correlations to be directly comparable among plots.

horiz.line

optionally, a numeric value indicating the y axis value for a horizontal threshold line to be drawn.

Value

This function returns a list.

Author(s)

A. Marcia Barbosa

See Also

binary.comparison

Examples

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## Not run: 
replicate.corrs <- repl.hs.comp(seqsubmats.hs = seqsubmats.hs, 
hs.baseline = hs.baseline, method = "Phi")

replicate.gains <- repl.hs.comp(seqsubmats.hs = seqsubmats.hs, 
hs.baseline = hs.baseline, method = "gain")

## End(Not run)

DeadCanMove documentation built on May 2, 2019, 6:48 p.m.