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.

Plot method for objects of class diffnet

Usage

Arguments

See also