Set node size and color from independent Cytoscape node attributes

Apply independent continuous visual mappings for node size and node color in the active Cytoscape network using columns from the node table. This helper is intended for PTMsToPathways-style networks where one node attribute controls size and a different attribute controls color.

Usage

setNodeSizeColorIndependently(sizeplotcol, colorplotcol, ratio = FALSE)

Arguments

sizeplotcol

A character string naming the node table column to use for node size mapping.

colorplotcol

A character string naming the node table column to use for node color mapping.

ratio

Logical; if TRUE, use predefined log2 ratio control points and ratio color palette. If FALSE, compute control points from the observed ranges of sizeplotcol and colorplotcol.

Value

This function is called for its side effects in Cytoscape and returns NULL invisibly.

Details

If either requested column is not present in the Cytoscape node table, the user is prompted to choose a valid column name interactively. For non-ratio data, color and size control points are derived from the observed ranges of the selected columns. For ratio-style data, fixed log2-based control points are used.

For ratio = FALSE, this function builds separate continuous mappings for node color and node size based on the minimum and maximum values observed in the selected Cytoscape node table columns. Blue-to-white-to-yellow color gradients are used for color mapping.

For ratio = TRUE, the function assumes ratio-like values centered on zero and applies fixed log2-scaled control points for both node size and node color. In this mode, a blue-to-green-to-yellow palette is used.

The function also locks node width and height and sets the default node selection color to magenta.

See also

RCy3::setNodeColorMapping(), RCy3::setNodeSizeMapping(), RCy3::lockNodeDimensions(), RCy3::getTableColumns()

Examples

if (FALSE) { # \dontrun{
setNodeSizeColorIndependently(
  sizeplotcol = "mean_expression",
  colorplotcol = "logFC",
  ratio = FALSE
)

setNodeSizeColorIndependently(
  sizeplotcol = "abundance_ratio",
  colorplotcol = "abundance_ratio",
  ratio = TRUE
)
} # }