plot refix and doc improvements

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Monarch Knowledge Graph Queries
 Description: R package for easy access, manipulation, and analysis of
 		Monarch KG data Resources.
-Version: 2.1.1
+Version: 2.1.2
 URL: https://github.com/monarch-initiative/monarchr
 BugReports: https://github.com/monarch-initiative/monarchr/issues
 Authors@R:
@@ -43,7 +43,7 @@ Imports:
     archive,
     readr,
     ggraph,
-    ggplot2,
+    ggplot2 (>= 4.0.0),
     R.utils,
     RCy3,
     digest,

NEWS.md

@@ -1,3 +1,10 @@
+# monarchr 2.1.2
+
+## Bug Fixes
+
+* Better fix for `edge_color`
+* Improved documentation for `transitive_closure()`, `transitive_reduction()`, `transfer()`, `roll_up()`, `roll_down()`
+
 # monarchr 2.1.1
 
 ## Bug Fixes

R/plot.tbl_kgx.R

@@ -5,7 +5,7 @@
 #' @param layout The layout to use for the plot. Default is "auto" as used by `ggraph`.
 #' @param node_color The column to use for node color. Default is "pcategory".
 #' @param node_shape The column to use for node shape Default is "namespace".
-#' @param edge_color The column to use for edge color. Default is NULL.
+#' @param edge_color The column to use for edge color. Default is "predicate".
 #' @param edge_linetype The column to use for edge line type. Default is "primary_knowledge_source".
 #' @param node_label The column to use for node labels. Defaults to "name".
 #' @param plot_ids Whether to show node IDs in node labels. Defaults to FALSE.
@@ -33,7 +33,7 @@ plot.tbl_kgx <- function(g,
 									layout = "auto",
 									node_color = pcategory,
 									node_shape = namespace,
-									edge_color = NULL,
+									edge_color = predicate,
 									edge_linetype = primary_knowledge_source,
 									node_label = name,
 									plot_ids = FALSE,

R/rollup.R

@@ -118,11 +118,15 @@ roll <- function(  column,
 #' @examples
 #' data(eds_marfan_kg)
 #'
-#' eds_marfan_kg |> fetch_nodes(name == "Tall stature" | name == "Short stature") |>
-#'   expand_n(predicates = "biolink:subclass_of", direction = "out", n = 2) |>  # get 2 levels of ancestors
+#' eds_marfan_kg |>
+#'   fetch_nodes(name == "Tall stature" | name == "Short stature") |>
+#'   # get 2 levels of ancestors
+#'   expand_n(predicates = "biolink:subclass_of", direction = "out", n = 2) |>
 #'   activate(nodes) |>
-#'   mutate(count = rpois(graph_order(), 1.5)) |>                               # random count value per node
-#'   mutate(sum_count = roll_up(count, fun = sum, include_self = TRUE)) |>      # apply sum to descendant (and self) values
+#'   # random count value per node
+#'   mutate(count = rpois(graph_order(), 1.5)) |>
+#'   # apply sum to descendant (and self) values
+#'   mutate(sum_count = roll_up(count, fun = sum, include_self = TRUE)) |>
 #'   plot(node_label = paste(name, " count: ", count, "sum_count: ", sum_count))
 #'
 #' @name rolling

R/transfer.R

@@ -12,15 +12,20 @@
 #'
 #' @return Vector or list, with one entry per node.
 #' @seealso [roll_up()], [transitive_closure], [descendants()], [ancestors()]
+#' @param colname The node column to transfer information from
+#' @param over The edge predicate to transfer information over
+#' @param direction Whether to transfer information along the predicate direction ("out") or against ("in")
 #'
 #' @examples
 #' data(eds_marfan_kg)
 #'
 #' engine |> eds_marfan_kg |>
 #' 	expand(categories = "biolink:Disease") |>
 #' 	activate(nodes) |>
-#' 	mutate(caused_by_genes = transfer(name, over = "biolink:causes", direction = "out")) |>
-#' 	mutate(causes_diseases = transfer(name, over = "biolink:causes", direction = "in")) |>
+#' 	mutate(caused_by_genes =
+#' 	         transfer(name, over = "biolink:causes", direction = "out")) |>
+#' 	mutate(causes_diseases =
+#' 	         transfer(name, over = "biolink:causes", direction = "in")) |>
 #' 	plot.tbl_kgx(node_label = paste(name,
 #' 																	" caused by: ", caused_by_genes,
 #' 																	" causes: ", causes_diseases),

R/transitive_closure.R

@@ -6,12 +6,15 @@
 #'
 #' @return Graph with transitive edges added.
 #' @seealso [roll_up()], [transfer()], [descendants()], [ancestors()]
+#' @param g The `tbl_kgx` graph to compute on.
+#' @param predicate The edge predicate to close over.
 #'
 #' @examples
 #' data(eds_marfan_kg)
 #'
 #' eds_marfan_kg |> fetch_nodes(name == "Tall stature") |>
-#'   expand_n(predicates = "biolink:subclass_of", direction = "out", n = 3) |>  # get 2 levels of ancestors
+#'   # get 2 levels of ancestors
+#'   expand_n(predicates = "biolink:subclass_of", direction = "out", n = 3) |>
 #'   activate(edges) |>
 #'   filter(primary_knowledge_source == "infores:upheno") |>
 #'   transitive_closure(predicate = "biolink:subclass_of") |>

R/transitive_reduction.R

@@ -5,13 +5,18 @@
 #'
 #' @return Graph with transitive edges added.
 #' @seealso [transitive_closure()], [roll_up()], [transfer()], [descendants()], [ancestors()]
+#' @param g The `tbl_kgx` graph to compute on.
+#' @param predicate The edge predicate to reduce over.
 #'
 #' @examples
 #' data(eds_marfan_kg)
 #'
 #' g <- eds_marfan_kg |> fetch_nodes(name == "Tall stature") |>
 #' 	expand_n(predicates = "biolink:subclass_of", direction = "out", n = 3) |>
-#' 	bind_edges(data.frame(from = 2, to = 9, predicate = "biolink_subclass_of", primary_knowledge_source = "hand_annotated"))
+#' 	bind_edges(data.frame(from = 2,
+#' 	                      to = 9,
+#' 	                      predicate = "biolink_subclass_of",
+#' 	                      primary_knowledge_source = "hand_annotated"))
 #'
 #' plot(g, edge_color = primary_knowledge_source)
 #'

README.md

@@ -2,7 +2,7 @@ monarchr
 ================
 [![License: MIT + file
 LICENSE](https://img.shields.io/badge/license-MIT%20+%20file%20LICENSE-blue.svg)](https://cran.r-project.org/web/licenses/MIT%20+%20file%20LICENSE)
-[![](https://img.shields.io/badge/devel%20version-2.1.1-black.svg)](https://github.com/monarch-initiative/monarchr)
+[![](https://img.shields.io/badge/devel%20version-2.1.2-black.svg)](https://github.com/monarch-initiative/monarchr)
 <br> [![R build
 status](https://github.com/monarch-initiative/monarchr/workflows/rworkflows/badge.svg)](https://github.com/monarch-initiative/monarchr/actions)
 [![](https://codecov.io/gh/monarch-initiative/monarchr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/monarch-initiative/monarchr)