diff --git a/R/cytoscapeNetwork.R b/R/cytoscapeNetwork.R index 7d492fb..51c2975 100644 --- a/R/cytoscapeNetwork.R +++ b/R/cytoscapeNetwork.R @@ -1,3 +1,4 @@ +```r # R/cytoscapeNetwork.R # # htmlwidgets binding for the Cytoscape network visualisation. @@ -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{ @@ -567,4 +568,5 @@ renderCytoscapeNetwork <- function(expr, env = parent.frame()) { env = env, quoted = TRUE ) -} \ No newline at end of file +} +``` \ No newline at end of file