Score matrix plot — matrixPlot • PhiSpace

Density and pairwise scatter plots for visualising score matrices.

matrixPlot(
  scores,
  max_ncomp = NULL,
  comp_idx = NULL,
  var_names = NULL,
  colBy = NULL,
  pointAlpha = NULL,
  pointSize = 1,
  manualCol = NULL,
  manualAlpha = NULL,
  fsize = 14,
  returnPlotList = F,
  legendTitle = "",
  compName = "comp",
  legendPosition = c("right", "left", "bottom", "top", "inside", "none")
)

Arguments

scores: Matrix of scores to be plotted
max_ncomp: Default NULL. Number of first components to plot. If specified, will override comp_idx and var_names.
comp_idx: Default NULL. Indices of components to plot. Will override var_names if specified.
var_names: Default NULL. Character vector of variable names (column names) to plot. Will be overridden by max_ncomp or comp_idx if they are specified.
colBy: Numeric or charactor vectors to specify colour of points.
pointAlpha: Alpha value.
pointSize: Point size.
manualCol: Manual specification of colours.
manualAlpha: Manual specification of alpha colours.
fsize: Figure font size.
returnPlotList: Logical. Whether to return individual plots.
legendTitle: Legend title.
compName: Name of the components, default is "comp", so that the 1st column is named comp1 etc.
legendPosition: Location of the legend when plotting two scores.