fusedMGM (version 0.1.2)

FMGM_plot: A plot function for a list of MGMs. The output is usually from FMGM main function.

Description

This function is written based on R base function 'heatmap'.

Usage

FMGM_plot(
  MGM_list,
  sortby = "diff",
  highlight = c(),
  tol_polish = 1e-12,
  tol_plot = 0.01,
  sideColor = FALSE,
  distfun = dist,
  hclustfun = hclust,
  reorderfun = function(d, w) reorder(d, w),
  margins = c(2.5, 2.5),
  cexRow = 0.1 + 0.5/log10(n),
  cexCol = cexRow,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  verbose = getOption("verbose")
)

Value

None

Arguments

MGM_list

A list of graphs from 2 groups. Usually a result of FMGM main function.

sortby

Determines the standard of sorting & dendrograms. Either 1, 2, or "diff" (default).

highlight

A vector of variable names or indices to highlight

tol_polish

A threshold for the network edge presence

tol_plot

Only network edges above this value will be displayed on the heatmap

sideColor

A named vector determining a sidebar colors. Set NULL to make the colors based on the variable types (discrete/continuous). Default: FALSE (no sidebars)

distfun

A function for the distances between rows/columns

hclustfun

A function for hierarchical clustering

reorderfun

A function of dendrogram and weights for reordering

margins

A numeric vector of 2 numbers for row & column name margins

cexRow

A visual parameter cex for row axis labeling

cexCol

A visual parameter cex for column axis labeling, default to be same as cexRow

main

Main title, default to none

xlab

X-axis title, default to none

ylab

Y-axis title, default to none

verbose

Logical. Should plotting information be printed?

Examples

chk <- tolower(Sys.getenv("_R_CHECK_LIMIT_CORES_", ""))

if (Sys.info()['sysname'] != 'Linux') {
  cores=1L
} else {
  chk = tolower(Sys.getenv("_R_CHECK_LIMIT_CORES_", ""))
  if (nzchar(chk) && (chk != "false")) {
    cores=2L
  } else {
    cores=parallel::detectCores() - 1 ;
  }
}

if (FALSE) {
data(data_all) ;  # Example 500-by-100 simulation data
data(ind_disc) ;

group <- rep(c(1,2), each=250) ;
names(group) <- seq(500) ;

res_FMGM <- FMGM_mc(data_all, ind_disc, group, 
                    lambda_intra=c(0.2,0.15,0.1), lambda_inter=c(0.2,0.15,0.1), 
                    cores=cores, verbose=TRUE)
                    
FMGM_plot(res_FMGM)
}

# \donttest{
data(data_mini) ; # Minimal example 500-by-10 simulation data
data(ind_disc_mini) ;

group <- rep(c(1,2), each=250) ;
names(group) <- rownames(data_mini) ;

res_FMGM_mini <- FMGM_mc(data_mini, ind_disc_mini, group, 
                    lambda_intra=c(0.2,0.15,0.1), lambda_inter=c(0.2,0.15,0.1), 
                    cores=cores, verbose=TRUE)
                    
FMGM_plot(res_FMGM_mini)
# }