tsplot: Time Series Plot

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

Time Series Plot

Description

Plot the time series row-wise.

Usage

tsplot(x, time.given = FALSE, num = nrow(x), sample.points = c(),
  mode = "lines", dist = "bray", my.color.map = list(),
  identifyPoints = FALSE, topN = 10, groups = c(),
  hideGroups = c(), legend = FALSE, labels = c(), noLabels = FALSE,
  centroid = FALSE, perturb = NULL, ...)

Arguments

x	the matrix of time series
time.given	if true, then the column names are supposed to hold the time units
num	the number of rows to plot (starting from the first row)
sample.points	indicate sample points (only for lines)
mode	lines (default), pcoa (a PCoA plot with arrows showing the community trajectory) or bars (a stacked barplot for each sample)
dist	the distance to use for the PCoA plot
my.color.map	map of taxon-specific colors, should match row names (only for bars) or group names (only for lines)
identifyPoints	click at points in the PCoA plot to identify them (using function identify), not active when noLabels is TRUE
topN	number of top taxa to be plotted for mode bars
groups	group membership vector; for mode bars and pcoa refers to samples; for mode lines refers to taxa; there are as many entries in the group membership vector as samples or taxa; taxa/samples are assumed to be ordered by groups
hideGroups	compute PCoA with all data, but do not show members of selected groups; expects one integer/name per group and consistency with groups parameter, only supported for mode pcoa
legend	add a legend
labels	use the provided labels in the PCoA plot
noLabels	do not use any labels in the PCoA plot
centroid	draw PCoA plot with a centroid (groups are ignored)
perturb	a perturbation object (adds polygons in mode lines highlighting the perturbation periods, colors labels in mode bars and colors dots in the PCoA plot)
\dots	Additional arguments passed to plot()

Examples

N=50
A=modifyA(generateA(N, c=0.1, d=-1),perc=70,strength="uniform",mode="negpercent")
out.ricker=ricker(N,A=A,y=generateAbundances(N,mode=5,prob=TRUE),K=rep(0.1,N), sigma=-1,tend=500)
tsplot(out.ricker, main="Ricker")
tsplot(out.ricker[,1:20],mode="bars",legend=TRUE)
tsplot(out.ricker[,1:50],mode="pcoa")

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.