rquipu: Creates quipu-type charts for a set of SSR markers

In c5sire/quipu: Summary Charts of Micro-Satellite Profiles for a Set of Biological Samples

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

rquipu(
  data,
  a.subset = c("all"),
  ylim = c(50, 350),
  res = c(1500, 1200),
  dir.print = getwd(),
  dir.logo = NA,
  col.node = c("red3", "green", "blue", "gray50"),
  col.marg = c("gray60", "black", "black"),
  species.name = NA,
  set.name = NA,
  img.format = "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"),
  show.size.range = TRUE,
  show.horizontal.lines = TRUE,
  vertical.lines.width = 2,
  show.desc = TRUE,
  lines.vertical.color = "grey90",
  ranges.color = "grey80",
  support.width = 2,
  support.color = "black"
)

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; default: current working directory
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, png, tiff); default 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'.
show.size.range	show or hide the allele size range on top of the vertical line
show.horizontal.lines	show or hide horizontal lines in the large layout
vertical.lines.width	line width of vertical lines; default is 2
show.desc	logical; show 'Description' box or not
lines.vertical.color	character; valid color name; default: grey90.
ranges.color	character; valid color name; default: grey80.
support.width	integer; width of uppper bar supporting hanging lines; default 1.
support.color	character; valid color name; default: black.

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

library(quipu)

data(potato.quipu)
dat = potato.quipu

str(dat)

rquipu(dat)

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


# This example produces high resolution output.
# It also shows more customization regarding colors and sizes of
# different elements.

if (interactive()) {
        rquipu(dat,
               layout="no text",
               img.format = "tiff",
               vertical.lines.width = 6,
               col.node = c("turquoise", "orange", "red", "purple"),
               lines.vertical.color = "wheat1",
               ranges.color = "wheat2", # allelic size range of set
               support.color = "wheat3",
               support.width = 8
        )     
}

c5sire/quipu documentation built on Nov. 14, 2020, 9:09 a.m.