Description Usage Arguments Details Author(s) Examples
The chart shows SSR marker weights on a linear scale where each allele or 'gel band' is represented by a circle. The circle's diameter can be sized and colored by its rareness. Two parameters 'col.fig' and 'grp.size'allow to do so. The 'rareness' can be calculated - by default - based only on the dataset at hand or by a supplied reference table. To do so, the parameter 'obs.alls.frq' expects a dataframe with three columns named 'Marker', 'Marker.Size' and 'Frequency'. Another parameter, 'obs.alls.frq.ref' should be used to supply a character string containing the reference to the source of allele frequencies being used. For visualization purposes, the class breaks can be defined using a vector of three numeric values in the range between 0 and 1 and be passed to the parameter 'grp.brks'. The default is 0.01, 0.05 and 0.001.
1 2 3 4 5 6 7 8 | rquipu(data, a.subset = c("all"), ylim = c(50, 350), res = c(1500, 1200),
dir.print = tempdir(), dir.logo = NA, col.node = c("red3", "green",
"blue", "gray50"), col.marg = c("gray60", "black", "black"),
species.name = NA, set.name = NA, img.format = c("screen", "jpeg",
"jpg", "png"), ltr.size = 0.8, show.accs.total = TRUE,
id.label = "Identifier", node.size = c(1.5, 1.2, 0.9, 0.6),
grp.brks = c(0.01, 0.05, 0.1), obs.alls.frq = NULL,
obs.alls.frq.ref = "dataset", layout = c("full", "no text"))
|
data |
a data.frame with minimal four columns: accession_id, primer_name, marker_size, map_location; alternatively, |
a.subset |
a vector of accession identifiers |
ylim |
the range of marker sizes (or alleles) in base pair (bp) units |
res |
the resolution of the final image in pixels (width, height) |
dir.print |
the directory to use for storing the created images |
dir.logo |
the path to a logo to display on the chart |
col.node |
colors for the chart elements |
col.marg |
colors for the chart margin elements |
species.name |
scientific name of the species of the set of accessions |
set.name |
a name for the set of accessions |
img.format |
specify a format for the final chart (jpeg or png) |
ltr.size |
letter size |
show.accs.total |
a logical value to show the number of accessions from the dataset |
id.label |
label for identifier |
node.size |
size of circle diameter for allele circles by frequency group |
grp.brks |
cut-off values between frequency groups; must be three values between 0 and 1 and in ascending order |
obs.alls.frq |
observed allele frequencies; format three-column data frame with heads: Marker, Marker.Size, Frequency. |
obs.alls.frq.ref |
a reference to the source of the allele frequencies |
layout |
whether a full chart or one without text; use 'full' or 'no text'. |
The chart was motivated by the need to represent genetic uniqueness of potato plant materials in a given set for a catalogue and the Andean tradition of quipus.
Reinhard Simon, Pablo Carhuapoma
1 2 3 4 5 6 7 8 9 10 | library(quipu)
data(potato.quipu)
dat = potato.quipu
str(dat)
rquipu(dat)
rquipu(dat, layout="no text", res=c(600,400))
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