plot.diffnet: Plot method for objects of class diffnet

In stefpeschel/NetCoMi: Network Construction and Comparison for Microbiome Data

Plot method for objects of class diffnet

Description

Plot method for objects of class diffnet

Usage

## S3 method for class 'diffnet'
plot(
  x,
  adjusted = TRUE,
  layout = NULL,
  repulsion = 1,
  labels = NULL,
  shortenLabels = "none",
  labelLength = 6,
  labelPattern = c(5, "'", 3, "'", 3),
  charToRm = NULL,
  labelScale = TRUE,
  labelFont = 1,
  rmSingles = TRUE,
  nodeColor = "gray90",
  nodeTransp = 60,
  borderWidth = 1,
  borderCol = "gray80",
  edgeFilter = "none",
  edgeFilterPar = NULL,
  edgeWidth = 1,
  edgeTransp = 0,
  edgeCol = NULL,
  title = NULL,
  legend = TRUE,
  legendPos = "topright",
  legendGroupnames = NULL,
  legendTitle = NULL,
  legendArgs = NULL,
  cexNodes = 1,
  cexLabels = 1,
  cexTitle = 1.2,
  cexLegend = 1,
  mar = c(2, 2, 4, 6),
  ...
)

Arguments

x	object of class diffnet (returned by diffnet) containing the adjacency matrix, whose entries are absolute differences between associations.
adjusted	logical indicating whether the adjacency matrix based on adjusted p-values should be used. Defaults to TRUE. If FALSE, the adjacency matrix is based on non-adjusted p-values. Ignored for the discordant method.
layout	indicates the layout used for defining node positions. Can be a character with one of the layouts provided by qgraph: "spring"(default), "circle", or "groups". Alternatively, the layouts provided by igraph (see layout\_) are accepted (must be given as character, e.g. "layout_with_fr"). Can also be a matrix with row number equal to the number of nodes and two columns corresponding to the x and y coordinate.
repulsion	integer specifying repulse radius in the spring layout; for a value lower than 1, nodes are placed further apart
labels	defines the node labels. Can be a character vector with an entry for each node. If FALSE, no labels are plotted. Defaults to the row/column names of the association matrices.
shortenLabels	character indicating how to shorten node labels. Ignored if node labels are defined via labels. NetCoMi's function editLabels() is used for label editing. Available options are: "intelligent" Elements of charToRm are removed, labels are shortened to length labelLength, and duplicates are removed using labelPattern. "simple" Elements of charToRm are removed and labels are shortened to length labelLength. "none" Default. Original dimnames of the adjacency matrices are used.
labelLength	integer defining the length to which labels shall be shortened if shortenLabels is set to "simple" or "intelligent". Defaults to 6.
labelPattern	vector of three or five elements, which is used if argument shortenLabels is set to "intelligent". If cutting a label to length labelLength leads to duplicates, the label is shortened according to labelPattern, where the first entry gives the length of the first part, the second entry is used a separator, and the third entry is the length of the third part. If labelPattern has five elements and the shortened labels are still not unique, the fourth element serves as further separator, and the fifth element gives the length of the last label part. Defaults to c(5, "'", 3, "'", 3). If the data contains, for example, three bacteria "Streptococcus1", "Streptococcus2" and "Streptomyces", they are by default shortened to "Strep'coc'1", "Strep'coc'2", and "Strep'myc".
charToRm	vector with characters to remove from node names. Ignored if labels are given via labels.
labelScale	logical. If TRUE, node labels are scaled according to node size
labelFont	integer defining the font of node labels. Defaults to 1.
rmSingles	logical. If TRUE, unconnected nodes are removed.
nodeColor	character or numeric value specifying node colors. Can also be a vector with a color for each node.
nodeTransp	an integer between 0 and 100 indicating the transparency of node colors. 0 means no transparency, 100 means full transparency. Defaults to 60.
borderWidth	numeric specifying the width of node borders. Defaults to 1.
borderCol	character specifying the color of node borders. Defaults to "gray80"
edgeFilter	character indicating whether and how edges should be filtered. Possible values are "none" (all edges are shown) and "highestDiff" (the first x edges with highest absolute difference are shown). x is defined by edgeFilterPar.
edgeFilterPar	numeric value specifying the "x" in edgeFilter.
edgeWidth	numeric specifying the edge width. See argument "edge.width" of qgraph.
edgeTransp	an integer between 0 and 100 indicating the transparency of edge colors. 0 means no transparency (default), 100 means full transparency.
edgeCol	character vector specifying the edge colors. Must be of length 6 for the discordant method (default: c("hotpink", "aquamarine", "red", "orange", "green", "blue")) and of lengths 9 for permutation tests and Fisher's z-test (default: c("chartreuse2", "chartreuse4", "cyan", "magenta", "orange", "red", "blue", "black", "purple")).
title	optional character string for the main title.
legend	logical. If TRUE, a legend is plotted.
legendPos	either a character specifying the legend's position or a numeric vector with two elements giving the x and y coordinates of the legend. See the description of the x and y arguments of legend for details.
legendGroupnames	a vector with two elements giving the group names shown in the legend.
legendTitle	character specifying the legend title.
legendArgs	list with further arguments passed to legend.
cexNodes	numeric scaling node sizes. Defaults to 1.
cexLabels	numeric scaling node labels. Defaults to 1.
cexTitle	numeric scaling the title. Defaults to 1.2.
cexLegend	numeric scaling the legend size. Defaults to 1.
mar	a numeric vector of the form c(bottom, left, top, right) defining the plot margins. Works similar to the mar argument in par. Defaults to c(2,2,4,6).
...	further arguments being passed to qgraph.

See Also

diffnet, netConstruct

stefpeschel/NetCoMi documentation built on Feb. 4, 2024, 8:20 a.m.