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Plot minimum spanning networks produced in poppr.

Source: R/visualizations.r
plot_poppr_msn.Rd

This function allows you to take the output of poppr.msn and bruvo.msn and customize the plot by labeling groups of individuals, size of nodes, and adjusting the palette and scale bar.

Usage

plot_poppr_msn(
  x,
  poppr_msn,
  gscale = TRUE,
  gadj = 3,
  mlg.compute = "original",
  glim = c(0, 0.8),
  gweight = 1,
  wscale = TRUE,
  nodescale = 10,
  nodebase = NULL,
  nodelab = 2,
  inds = "ALL",
  mlg = FALSE,
  quantiles = TRUE,
  cutoff = NULL,
  palette = NULL,
  layfun = layout.auto,
  beforecut = FALSE,
  pop.leg = TRUE,
  size.leg = TRUE,
  scale.leg = TRUE,
  ...
)

Arguments

x

a genind, genclone, genlight, or snpclone object from which poppr_msn was derived.

poppr_msn

a list produced from either poppr.msn or bruvo.msn. This list should contain a graph, a vector of population names and a vector of hexadecimal color definitions for each population.

gscale

"grey scale". If this is TRUE, this will scale the color of the edges proportional to the observed distance, with the lines becoming darker for more related nodes. See greycurve for details.

gadj

"grey adjust". a positive integer greater than zero that will serve as the exponent to the edge weight to scale the grey value to represent that weight.

mlg.compute

if the multilocus genotypes are set to "custom" (see mll.custom for details) in your genclone object, this will specify which mlg level to calculate the nodes from. See details.

glim

"grey limit". Two numbers between zero and one. They determine the upper and lower limits for the gray function. Default is 0 (black) and 0.8 (20% black).

gweight

"grey weight". an integer. If it's 1, the grey scale will be weighted to emphasize the differences between closely related nodes. If it is 2, the grey scale will be weighted to emphasize the differences between more distantly related nodes.

wscale

"width scale". If this is TRUE, the edge widths will be scaled proportional to the inverse of the observed distance , with the lines becoming thicker for more related nodes.

nodescale

a numeric indicating how to scale the node sizes (scales by area).

nodebase

deprecated a numeric indicating what base logarithm should be used to scale the node sizes. Defaults to 1.15. See details.

nodelab

an integer specifying the smallest size of node to label. See details.

inds

a character or numeric vector indicating which samples or multilocus genotypes to label on the graph. See details.

mlg

logical When TRUE, the nodes will be labeled by multilocus genotype. When FALSE (default), nodes will be labeled by sample names.

quantiles

logical. When set to TRUE (default), the scale bar will be composed of the quantiles from the observed edge weights. When set to FALSE, the scale bar will be composed of a smooth gradient from the minimum edge weight to the maximum edge weight.

cutoff

a number indicating the longest distance to display in your graph. This is performed by removing edges with weights greater than this number.

palette

a function or character corresponding to a specific palette you want to use to delimit your populations. The default is whatever palette was used to produce the original graph.

layfun

a function specifying the layout of nodes in your graph. It defaults to layout.auto.

beforecut

if TRUE, the layout of the graph will be computed before any edges are removed with cutoff. If FALSE (Default), the layout will be computed after any edges are removed.

pop.leg

if TRUE, a legend indicating the populations will appear in the top right corner of the graph, but will not overlap. Setting pop.leg = FALSE disables this legend. See details.

size.leg

if TRUE, a legend displyaing the number of samples per node will appear either below the population legend or in the top right corner of the graph. Setting size.leg = FALSE disables this legend.

scale.leg

if TRUE, a scale bar indicating the distance will appear under the graph. Setting scale.leg = FALSE suppresses this bar. See details.

...

any other parameters to be passed on to plot.igraph.

Value

the modified msn list, invisibly.

Details

The previous incarnation of msn plotting in poppr simply plotted the minimum spanning network with the legend of populations, but did not provide a scale bar and it did not provide the user a simple way of manipulating the layout or labels. This function allows the user to manipulate many facets of graph creation, making the creation of minimum spanning networks ever so slightly more user friendly.

This function must have both the source data and the output msn to work. The source data must contain the same population structure as the graph. Every other parameter has a default setting.

Parameter details

  • inds By default, the graph will label each node (circle) with all of the samples (individuals) that are contained within that node. As each node represents a single multilocus genotype (MLG) or individuals (n >= 1), this argument is designed to allow you to selectively label the nodes based on query of sample name or MLG number. If the option mlg = TRUE, the multilocus genotype assignment will be used to label the node. If you do not want to label the nodes by individual or multilocus genotype, simply set this to a name that doesn't exist in your data.

  • nodescale The nodes (circles) on the graph represent different multilocus genotypes. The area of the nodes represent the number of individuals. Setting nodescale will scale the area of the nodes.

  • nodelab If a node is not labeled by individual, this will label the size of the nodes greater than or equal to this value. If you don't want to label the size of the nodes, simply set this to a very high number.

  • cutoff This is useful for when you want to investigate groups of multilocus genotypes separated by a specific distance or if you have two distinct populations and you want to physically separate them in your network.

  • beforecut This is an indicator useful if you want to maintain the same position of the nodes before and after removing edges with the cutoff argument. This works best if you set a seed before you run the function.

mlg.compute

Each node on the graph represents a different multilocus genotype. The edges on the graph represent genetic distances that connect the multilocus genotypes. In genclone objects, it is possible to set the multilocus genotypes to a custom definition. This creates a problem for clone correction, however, as it is very possible to define custom lineages that are not monophyletic. When clone correction is performed on these definitions, information is lost from the graph. To circumvent this, The clone correction will be done via the computed multilocus genotypes, either "original" or "contracted". This is specified in the mlg.compute argument, above.

legends

To avoid drawing the legend over the graph, legends are separated by different plotting areas. This means that if legends are included, you cannot plot multiple MSNs in a single plot. The scale bar (to be added in manually) can be obtained from greycurve and the legend can be plotted with legend.

See also

layout.auto plot.igraph poppr.msn bruvo.msn greycurve delete_edges palette

Author

Zhian N. Kamvar

Examples

# Using a data set of the Aphanomyces eutieches root rot pathogen.
data(Aeut)
adist <- diss.dist(Aeut, percent = TRUE)
amsn <- poppr.msn(Aeut, adist, showplot = FALSE)

# Default
library("igraph") # To get all the layouts.
#> 
#> Attaching package: ‘igraph’
#> The following objects are masked from ‘package:ape’:
#> 
#>     degree, edges, mst, ring
#> The following objects are masked from ‘package:stats’:
#> 
#>     decompose, spectrum
#> The following object is masked from ‘package:base’:
#> 
#>     union
set.seed(500)
plot_poppr_msn(Aeut, amsn, gadj = 15)


# \dontrun{

# Different layouts (from igraph) can be used by supplying the function name.
set.seed(500)
plot_poppr_msn(Aeut, amsn, gadj = 15, layfun = layout_with_kk)


# Removing link between populations (cutoff = 0.2) and labelling no individuals
set.seed(500)
plot_poppr_msn(Aeut, amsn, inds = "none", gadj = 15, beforecut = TRUE, cutoff = 0.2)


# Labelling individual #57 because it is an MLG that crosses populations
# Showing clusters of MLGS with at most 5% variation
# Notice that the Mt. Vernon population appears to be more clonal
set.seed(50) 
plot_poppr_msn(Aeut, amsn, gadj = 15, cutoff = 0.05, inds = "057")



data(partial_clone)
pcmsn <- bruvo.msn(partial_clone, replen = rep(1, 10))


# You can plot using a color palette or a vector of named colors
# Here's a way to define the colors beforehand
pc_colors <- nPop(partial_clone) %>% 
  RColorBrewer::brewer.pal("Set2") %>% 
  setNames(popNames(partial_clone))

pc_colors
#>         1         2         3         4 
#> "#66C2A5" "#FC8D62" "#8DA0CB" "#E78AC3" 

# Labelling the samples contained in multilocus genotype 9
set.seed(999)
plot_poppr_msn(partial_clone, pcmsn, palette = pc_colors, inds = 9)

# Doing the same thing, but using one of the sample names as input.
set.seed(999)
plot_poppr_msn(partial_clone, pcmsn, palette = pc_colors, inds = "sim 20")


# Note that this is case sensitive. Nothing is labeled. 
set.seed(999)
plot_poppr_msn(partial_clone, pcmsn, palette = pc_colors, inds = "Sim 20")


# Something pretty
data(microbov)
mdist <- diss.dist(microbov, percent = TRUE)
micmsn <- poppr.msn(microbov, mdist, showplot = FALSE)

plot_poppr_msn(microbov, micmsn, palette = "terrain.colors", inds = "n", 
  quantiles = FALSE)

plot_poppr_msn(microbov, micmsn, palette = "terrain.colors", inds = "n", 
  cutoff = 0.3, quantiles = FALSE)

  
### Utilizing vectors for palettes

data(Pram)
Pram_sub <- popsub(Pram, exclude = c("Nursery_CA", "Nursery_OR"))

# Creating the network for the forest
min_span_net_sub <- bruvo.msn(Pram_sub, replen = other(Pram)$REPLEN, 
                              add = TRUE, loss = TRUE, showplot = FALSE, 
                              include.ties = TRUE)
                              
# Creating the network with nurseries
min_span_net     <- bruvo.msn(Pram, replen = other(Pram)$REPLEN, 
                              add = TRUE, loss = TRUE, showplot = FALSE, 
                              include.ties = TRUE)

# Only forest genotypes
set.seed(70)
plot_poppr_msn(Pram,
               min_span_net_sub,
               inds = "ALL",
               mlg = TRUE,
               gadj = 9,
               nodescale = 5,
               palette = other(Pram)$comparePal,
               cutoff = NULL,
               quantiles = FALSE,
               beforecut = TRUE)


# With Nurseries
set.seed(70)
plot_poppr_msn(Pram,
               min_span_net,
               inds = "ALL",
               mlg = TRUE,
               gadj = 9,
               nodescale = 5,
               palette = other(Pram)$comparePal,
               cutoff = NULL,
               quantiles = FALSE,
               beforecut = TRUE)

# }