plot.net: Plotting a network

In SFSI: Sparse Family and Selection Index

Plotting a network

Description

Plot a Graphical Network obtained from a numeric matrix

Usage

## S3 method for class 'net'
plot(x, i = NULL, show.names = FALSE,
        group = NULL, group.shape = NULL,
        set.color = NULL, set.size = NULL,
        axis.labels = TRUE, curve = FALSE,
        bg.color = "white", unified = TRUE, ni = 36,
        line.color = "gray70", line.tick = 0.3,
        legend.pos = "right", point.color = "gray20",
        sets = c("Testing","Supporting","Non-active"),
        circle = FALSE, ...)

Arguments

x	An object of the 'net' class as per the net function
i	(integer vector) Index subjects in rows to be shown in plot. Default i=NULL will consider all elements in rows
show.names	TRUE or FALSE to whether show node names given by the row/column names of the matrix used to make the net (see help(net))
group	(data.frame) Column grouping for the subjects
group.shape	(integer vector) Shape of each level of the grouping column provided as group
bg.color	(character) Plot background color
line.color	(character) Color of lines connecting nodes in rows with those in columns
line.tick	(numeric) Tick of lines connecting nodes in rows with those in columns
curve	TRUE or FALSE to whether draw curve lines connecting nodes in rows with those in columns
set.color	(character vector) Color point of each type of node: row, 'active' column, and 'non-active' column, respectively
set.size	(numeric vector) Size of each type of node: row, 'active' column, and 'non-active' column, respectively
axis.labels	TRUE or FALSE to whether show labels in both axes
unified	TRUE or FALSE to whether show an unified plot or separated for each individual in 'testing'
point.color	(character) Color of the points in the plot
ni	(integer) Maximum number of row nodes that are plotted separated as indicated by unified=FALSE
legend.pos	(character) Either "right", topright","bottomleft","bottomright","topleft", or "none" indicating where the legend is positioned in the plot
sets	(character vector) Names of the types of node: row, 'active' column, and 'non-active' column, respectively
circle	TRUE or FALSE to whether draw a circle for each trait in a Multi-trait 'SSI'
...	Other arguments for method plot: 'xlab', 'ylab', 'main'

Details

Plot a Graphical Network from a matrix where nodes are subjects in the rows and columns, and edges are obtained from the matrix entries. This Network is obtained using net function

Examples

  require(SFSI)
  data(wheatHTP)
  
  #--------------------------------------
  # Net for an SSI object
  #--------------------------------------
  index = which(Y$trial %in% 1:6)     # Use only a subset of data
  Y = Y[index,]
  M = scale(M[index,])/sqrt(ncol(M))  # Subset and scale markers
  G = tcrossprod(M)                   # Genomic relationship matrix
  y = as.vector(scale(Y[,"E1"]))      # Scale response variable
  
  trn_tst = ifelse(Y$trial == 2, 0, 1)

  fm = SSI(y,K=G,trn_tst=trn_tst)
  
  tmp = net(fm)          # Get the net
  plot(tmp)              # Plot the net
  plot(tmp, i=c(1,2))    # Show the first and fifth tst elements
  plot(net(fm, nsup=10), show.names=c(TRUE,TRUE,FALSE))
  
  #--------------------------------------
  # Net for a numeric matrix
  #--------------------------------------
  B = as.matrix(coef(fm, nsup=10))
  plot(net(B), curve=TRUE, set.size=c(3.5,1.5,1))
  
  #--------------------------------------
  # Net for a symmetric numeric matrix
  #--------------------------------------
  X = X_E1[,seq(1,ncol(X_E1),by=5)]
  R2 = cor(X)^2  # An R2 matrix
  plot(net(R2, delta=0.9))
  

SFSI documentation built on Nov. 18, 2023, 9:06 a.m.