From d2e027e48d1a4bec3e1a3e2831fe1a3c3746bc8c Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Fri, 20 Oct 2023 12:50:52 -0400
Subject: [PATCH] update: sankey plotting

- param reorganization
- allow sankey plotting directly from a data.frame of relationships
---
 R/plot_sankey.R   | 56 ++++++++++++++++++++++++++++++++++++-----------
 man/sankeyPlot.Rd | 15 +++++++++----
 2 files changed, 54 insertions(+), 17 deletions(-)

diff --git a/R/plot_sankey.R b/R/plot_sankey.R
index 8d53320..ffbc2cc 100644
--- a/R/plot_sankey.R
+++ b/R/plot_sankey.R
@@ -50,7 +50,7 @@ setMethod('show', signature = 'giottoSankeyPlan', function(object) {
 # generics ####
 setGeneric('sankeyRelate', function(x, ...) standardGeneric('sankeyRelate'))
 setGeneric('sankeyRelate<-', function(x, add, value) standardGeneric('sankeyRelate<-'))
-setGeneric('sankeyPlot', function(gobject, x, ...) standardGeneric('sankeyPlot'))
+setGeneric('sankeyPlot', function(x, y, ...) standardGeneric('sankeyPlot'))
 
 
 # methods ####
@@ -447,8 +447,9 @@ sankey_relation_pair = function(g, gsp, rel_idx, node_idx_start = 0) {
 #' and (optionally) `idx` params. More complex and cross spatial unit/feature
 #' type sankeys can be set up using the `sankey_plan` param which accepts a
 #' `giottoSankeyPlan` object.
-#' @inheritParams data_access_params
-#' @param x giottoSankeyPlan object or character vector referring to source and
+#' @param x data source (gobject or data.frame-like object with relations
+#' between the first two cols provided)
+#' @param y giottoSankeyPlan object or character vector referring to source and
 #' target columns in metadata
 #' @param meta_type build sankey on cell or feature metadata
 #' @param spat_unit spatial unit of metadata
@@ -458,6 +459,9 @@ sankey_relation_pair = function(g, gsp, rel_idx, node_idx_start = 0) {
 #' @inheritDotParams networkD3::sankeyNetwork -Links -Nodes -Source -Target -Value -NodeID
 #' @examples
 #' \dontrun{
+#' x = data.table::data.table(col1 = c('a', 'a', 'b'),
+#'                            col2 = c('x', 'y', 'y'))
+#' sankeyPlot(x)
 #' g = GiottoData::loadGiottoMini("vizgen")
 #' # with giottoSankeyPlan
 #' leiden = sankeySet(spat_unit = 'aggregate',
@@ -483,13 +487,12 @@ sankey_relation_pair = function(g, gsp, rel_idx, node_idx_start = 0) {
 #' @export
 setMethod(
   'sankeyPlot',
-  signature(gobject = 'giotto',
-            x = 'giottoSankeyPlan'),
-  function(gobject,
-           x,
+  signature(x = 'giotto',
+            y = 'giottoSankeyPlan'),
+  function(x,
+           y,
            meta_type = c('cell', 'feat'),
            ...) {
-    checkmate::assert_class(gobject, 'giotto')
     GiottoUtils::package_check("networkD3")
     meta_type = match.arg(meta_type, choices = c('cell', 'feat'))
     x@data_type = meta_type
@@ -537,17 +540,18 @@ setMethod(
 #' @export
 setMethod(
   'sankeyPlot',
-  signature(gobject = 'giotto',
-            x = 'character'),
-  function(gobject,
-           x,
+  signature(x = 'giotto',
+            y = 'character'),
+  function(x,
+           y,
            spat_unit = NULL,
            feat_type = NULL,
            meta_type = c('cell', 'feat'),
            idx = NULL,
            ...) {
 
-    checkmate::assert_character(x, len = 2L)
+    GiottoUtils::package_check("networkD3")
+    checkmate::assert_character(y, len = 2L)
 
     # Data type being compared. Either cell or feat
     meta_type = match.arg(meta_type, choices = c('cell', 'feat'))
@@ -601,3 +605,29 @@ setMethod(
   }
 )
 
+
+#' @rdname sankeyPlot
+#' @export
+setMethod('sankeyPlot', signature(x = 'data.frame', y = 'missing'), function(x, ...) {
+  GiottoUtils::package_check("networkD3")
+
+  res = sankey_compare(data_dt = x)
+  links_dt = res$links
+
+  # create nodes table
+  nodes = data.table::data.table(name = res$nodes)
+
+  networkD3::sankeyNetwork(
+    Links = links_dt,
+    Nodes = nodes,
+    Source = 'source',
+    Target = 'target',
+    Value = 'value',
+    NodeID = 'name',
+    ...
+  )
+
+})
+
+
+
diff --git a/man/sankeyPlot.Rd b/man/sankeyPlot.Rd
index 528679f..9dee432 100644
--- a/man/sankeyPlot.Rd
+++ b/man/sankeyPlot.Rd
@@ -3,24 +3,28 @@
 \name{sankeyPlot}
 \alias{sankeyPlot}
 \alias{sankeyPlot,giotto,character-method}
+\alias{sankeyPlot,data.frame,missing-method}
 \title{Create a sankey plot}
 \usage{
-\S4method{sankeyPlot}{giotto,giottoSankeyPlan}(gobject, x, meta_type = c("cell", "feat"), ...)
+\S4method{sankeyPlot}{giotto,giottoSankeyPlan}(x, y, meta_type = c("cell", "feat"), ...)
 
 \S4method{sankeyPlot}{giotto,character}(
-  gobject,
   x,
+  y,
   spat_unit = NULL,
   feat_type = NULL,
   meta_type = c("cell", "feat"),
   idx = NULL,
   ...
 )
+
+\S4method{sankeyPlot}{data.frame,missing}(x, y, ...)
 }
 \arguments{
-\item{gobject}{giotto object}
+\item{x}{data source (gobject or data.frame-like object with relations
+between the first two cols provided)}
 
-\item{x}{giottoSankeyPlan object or character vector referring to source and
+\item{y}{giottoSankeyPlan object or character vector referring to source and
 target columns in metadata}
 
 \item{meta_type}{whether to use 'cell' (cell) or 'feat' (feature) metadata}
@@ -71,6 +75,9 @@ type sankeys can be set up using the \code{sankey_plan} param which accepts a
 }
 \examples{
 \dontrun{
+x = data.table::data.table(col1 = c('a', 'a', 'b'),
+                           col2 = c('x', 'y', 'y'))
+sankeyPlot(x)
 g = GiottoData::loadGiottoMini("vizgen")
 # with giottoSankeyPlan
 leiden = sankeySet(spat_unit = 'aggregate',