Merge pull request #71 from cns-iu/pbi-get-organ-label-for-ref-organ

Added code to add label to reference organ

ctpop_plots/PlotsPaper.R

@@ -316,9 +316,14 @@ rui_count = more_cols %>% count (as_id)
 more_cols = merge(more_cols, rui_count, by.x = "as_id")
 colnames(more_cols)[colnames(more_cols) == "n"] <- "rui_locations_per_as"
 
-p = ggplot(more_cols, aes(x = reorder(as_label, -intersection_volume), y = intersection_volume, fill=sex, alpha = rui_locations_per_as))+
+# add tissue_block_intersection_percentage
+with_ratio = more_cols %>% mutate(
+  tissue_block_intersection_percentage = intersection_volume/tissue_block_volume
+)
+
+p = ggplot(with_ratio, aes(x = organ_label, y = tissue_block_intersection_percentage, fill=sex, alpha = rui_locations_per_as))+
   geom_bar(stat = "identity")+
-  facet_wrap(~organ)+
+  # facet_wrap(~organ_label)+
   scale_y_continuous(labels=scales::number_format(decimal.mark = '.'))+
   scale_color_brewer()+
   scale_fill_brewer(type="qual", palette = "Dark2")+

data-processor/queries/table-s5.rq

@@ -15,8 +15,11 @@ PREFIX dc: <http://purl.org/dc/terms/>
 PREFIX hubmap: <https://entity.api.hubmapconsortium.org/entities/>
 PREFIX rui: <http://purl.org/ccf/1.5/>
 
-SELECT DISTINCT ?rui_location ?organ ?as_label ?as_id ?intersection_volume ?as_volume ?tissue_block_volume
+SELECT DISTINCT ?rui_location ?organ ?organ_label ?as_label ?as_id ?intersection_volume ?as_volume ?tissue_block_volume
+
 FROM ctpop-graph:
+FROM <https://purl.org/ccf/releases/2.2.1/ccf.owl>
+
 WHERE {
 
 	    # Get tissue block volume
@@ -36,8 +39,16 @@ WHERE {
 					ccf:has_reference_organ ?ref_organ ;
 					ccf:percentage_of_total ?percentage ;
     	]
-    ]
+    ] .
+
+	# get label for reference organ
+	?ref_organ ccf:representation_of ?organId .
+    ?organId rdfs:label ?organ_label
+
 		BIND (?tissue_block_volume * ?percentage as ?intersection_volume)
   	BIND (REPLACE(REPLACE(REPLACE(STR(?ref_organ), "http://purl.org/ccf/latest/ccf.owl#", ""), "Colon", "LargeIntestine"), "V1.1", "") as ?organ)
+
+
+
 }
 ORDER BY ?organ ?rui_location DESC(?as_volume)