Merge pull request #79 from monarch-initiative/appnotes

Some fixes for #80 and #82

Author: oneilsh

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
+Version: 2.1.1
 URL: https://github.com/monarch-initiative/monarchr
 BugReports: https://github.com/monarch-initiative/monarchr/issues
 Authors@R:

NEWS.md

@@ -1,3 +1,11 @@
+# monarchr 2.1.1
+
+## Bug Fixes
+
+* Fixed a bug in `file_engine` `expand()` not including the query graph on transitive expansions
+* Temporarily set `edge_color` default to `NULL` until `ggplot` 4.0.1 is released with [this](https://github.com/tidyverse/ggplot2/issues/6669) bugfix
+* Update badges
+
 # monarchr 2.1
 
 ## New features

R/expand_file_engine.R

@@ -49,6 +49,8 @@ transitive_query_internal <- function(engine,
             filter(purrr::map_lgl(category, ~ any(.x %in% categories)) | id %in% query_ids)
     }
 
+    suppressMessages(bfs_result <- kg_join(g, bfs_result), classes = "message")
+
     attr(bfs_result, "last_engine") <- engine
     return(bfs_result)
 }

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 "predicate".
+#' @param edge_color The column to use for edge color. Default is NULL.
 #' @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 = predicate,
+									edge_color = NULL,
 									edge_linetype = primary_knowledge_source,
 									node_label = name,
 									plot_ids = FALSE,

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-1.5.0-black.svg)](https://github.com/monarch-initiative/monarchr)
+[![](https://img.shields.io/badge/devel%20version-2.1.1-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)

man/plot.tbl_kgx.Rd

@@ -4,7 +4,8 @@ library(assertthat)
 test_that("neo4j_engine caching", {
   e <- neo4j_engine(url = c("http://neo4j.monarchinitiative.org:7474",
   													"http://neo4j.monarchinitiative.org",
-                            "http://no.such.url"),
+  													"https://neo4j.monarchinitiative.org",
+  													"http://no.such.url"),
   									cache = TRUE)
 
   		start_time <- Sys.time()
@@ -37,6 +38,7 @@ test_that("neo4j_engine works as expected (using monarch neo4j db)", {
 
     # one of these should work
     e <- neo4j_engine(url = c("http://neo4j.monarchinitiative.org",
+    													"https://neo4j.monarchinitiative.org",
                               "http://no.such.url",
                               "http://neo4j.monarchinitiative.org:7474"))
 

tests/testthat/test-neo4j_engine.R

@@ -45,8 +45,8 @@ library(dplyr)
 data(eds_marfan_kg)
 
 g <- eds_marfan_kg |> fetch_nodes(query_ids = "HP:0001788") |> 
-	expand(categories = "biolink:Disease") |>
-	expand(categories = "biolink:Gene")
+  expand(categories = "biolink:Disease") |>
+  expand(categories = "biolink:Gene")
 
 nodes(g) |> select(id, name, pcategory, category)
 ```
@@ -60,12 +60,12 @@ We can adjust this when initializing the engine. To do so in this example we nee
 filename <- filename <- system.file("extdata", "eds_marfan_kg.tar.gz", package = "monarchr")
 
 eds_marfan_kg <- file_engine(filename, 
-								             preferences = list(category_priority = c("biolink:GenomicEntity", 
+                             preferences = list(category_priority = c("biolink:GenomicEntity", 
 								             																				 "biolink:DiseaseOrPhenotypicFeature")))
 
 g <- eds_marfan_kg |> fetch_nodes(query_ids = "HP:0001788") |> 
-	expand(categories = "biolink:Disease") |>
-	expand(categories = "biolink:Gene")
+  expand(categories = "biolink:Disease") |>
+  expand(categories = "biolink:Gene")
 
 nodes(g) |> select(id, name, pcategory, category)
 ```
@@ -89,10 +89,10 @@ constructor:
 monarch <- monarch_engine(cache = FALSE)
 
 g1 <- monarch |> fetch_nodes(query_ids = "HP:0001788") |>
-	expand()
+  expand()
 
 g2 <- monarch |> fetch_nodes(query_ids = "HP:0001788") |>
-	expand()
+  expand()
 ```
 
 In the above example, because caching is disabled, the fetch and expansion are re-run in computing `g2`.