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docs: Weekly AI doc upgrade for cytoscapeNetwork #85

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38 changes: 20 additions & 18 deletions R/cytoscapeNetwork.R
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
```r
# R/cytoscapeNetwork.R
#
# htmlwidgets binding for the Cytoscape network visualisation.
Expand Down Expand Up @@ -368,29 +369,29 @@
#' Render a Cytoscape network visualisation
#'
#' Creates an interactive network diagram powered by Cytoscape.js and the dagre
#' layout algorithm. Nodes can carry log fold-change (logFC) values which are
#' mapped to a blue-grey-red colour gradient. PTM (post-translational
#' layout algorithm. Nodes can carry log fold-change (logFC) values which are
#' mapped to a blue-grey-red colour gradient. PTM (post-translational
#' modification) site information is shown as small satellite nodes and edge
#' overlaps are surfaced as hover tooltips.
#'
#' @param nodes Data frame with at minimum an \code{id} column. Optional
#' columns: \code{logFC} (numeric), \code{hgncName}
#' (character), \code{Site} (character, underscore-separated
#' PTM site list).
#' @param edges Data frame with columns \code{source}, \code{target},
#' \code{interaction}. Optional: \code{site},
#' \code{evidenceLink}.
#' @param nodes \code{data.frame} with at minimum an \code{id} column. Optional
#' columns: \code{logFC} (\code{numeric}), \code{hgncName} (\code{character}),
#' \code{Site} (\code{character}, underscore-separated PTM site list).
#' @param edges \code{data.frame} with columns \code{source}, \code{target},
#' \code{interaction}. Optional: \code{site}, \code{evidenceLink}.
#' @param displayLabelType \code{"id"} (default) or \code{"hgncName"} –
#' controls which column is used as the visible node label.
#' @param nodeFontSize Font size (px) for node labels. Default \code{12}.
#' @param layoutOptions Named list of dagre layout options to override the
#' defaults (e.g. \code{list(rankDir = "LR")}).
#' @param width,height Widget dimensions passed to
#' \code{\link[htmlwidgets]{createWidget}}.
#' @param elementId Optional explicit HTML element id.
#' controls which column is used as the visible node label.
#' @param nodeFontSize \code{numeric} Font size (px) for node labels. Default \code{12}.
#' @param layoutOptions \code{list} Named list of dagre layout options to override the
#' defaults (e.g. \code{list(rankDir = "LR")}).
#' @param width \code{numeric} or \code{character} Widget width passed to
#' \code{\link[htmlwidgets]{createWidget}}.
#' @param height \code{numeric} or \code{character} Widget height passed to
#' \code{\link[htmlwidgets]{createWidget}}.
#' @param elementId \code{character} Optional explicit HTML element id.
#'
#' @return An \code{htmlwidget} object that renders in R Markdown, Shiny, or
#' the RStudio Viewer pane.
#' the RStudio Viewer pane.
#'
#' @examples
#' \dontrun{
Expand Down Expand Up @@ -567,4 +568,5 @@ renderCytoscapeNetwork <- function(expr, env = parent.frame()) {
env = env,
quoted = TRUE
)
}
}
```