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Plot an adjacency or incidence Matrix

Source: R/plotMyMatrix.R
plotMyMatrix.Rd

Plot an adjacency or incidence Matrix

Usage

plotMyMatrix(
  Mat,
  dimLabels = c(row = "row", col = "col"),
  clustering = NULL,
  plotOptions = NULL
)

Arguments

Mat

: a matrix representing the network

dimLabels

: a vector of length 1 or 2 specifying the types of nodes in row and col (functional group) (Default is NULL)

clustering

: a list of length 2 specifying a clustering on row and col

plotOptions

: a list providing options. See details below.

Value

a ggplot object corresponding to the plot

Details

The list of parameters plotOptions for the matrix plot is

  • "legend": Boolean. Set TRUE if you want to see the legend. Default value is FALSE

  • "legend.title": Boolean. Set TRUE if you want to print the title of the legend. Default value is FALSE

  • "legend.position": Position of the legend. Possible values are 'bottom', 'top','left,'right'. Default value is 'bottom'

  • "rowNames": Set true if the rownames must be plotted. Default value is FALSE

  • "colNames": Set true if the colNames must be plotted. Default value is FALSE

  • "names.size": Numeric. Size (in pts) of the row and column names. Default value is NULL: the size decreases with the number of nodes, so that the names do not overlap on a 5 inches plot

  • "line.color": Chain of character. The color of the lines to separate groups if a clustering is provided. Default value is red

  • "line.width": Numeric. Width of the lines to separate groups. Default value is NULL, automatically chosen

  • "title": Chain of character. Title of the plot. Default value is NULL

  • "blockBackground": Boolean. Color the background of each block, with an opacity growing with the mean value of the entries in the block. Only used when a clustering is provided. Default value is TRUE

  • "block.color": Chain of character. The color of the block background. Default value is red

  • "blockAlpha.min", "blockAlpha.max": Numeric. Opacity of the least and most dense blocks. Default values are 0.1 and 0.6

Examples

M <- matrix(sample(c(0,1),900,replace=TRUE),30,30)
plotMyMatrix(M, dimLabels = c('individulals'), plotOptions= list(legend = FALSE))

M2 <- matrix( rpois(800,10),40,20)
plotMyMatrix(M2, dimLabels = c(row = 'reader',col = 'book'), plotOptions = list(legend = TRUE))