Creates quipu-type charts for a set of SSR markers

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Description

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.

Usage

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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"))

Arguments

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'.

Details

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.

Author(s)

Reinhard Simon, Pablo Carhuapoma

Examples

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library(quipu)

data(potato.quipu)
dat = potato.quipu

str(dat)

rquipu(dat)

rquipu(dat, layout="no text", res=c(600,400))