From e5bfdbe8844786c6192c5c58c72d4dbd5f4fe2f8 Mon Sep 17 00:00:00 2001
From: Marek Ostaszewski <marek.ostaszewski@uni.lu>
Date: Mon, 8 Jun 2020 08:18:02 +0200
Subject: [PATCH] Alias resolver
---
Resources/Hipathia/resolve_aliases.R | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/Resources/Hipathia/resolve_aliases.R b/Resources/Hipathia/resolve_aliases.R
index 1e26160..aff57b6 100644
--- a/Resources/Hipathia/resolve_aliases.R
+++ b/Resources/Hipathia/resolve_aliases.R
@@ -52,7 +52,7 @@ this_refs <- models[models$name == diag_name]
### Get elements of the chosen diagram
model_elements <- fromJSON(ask_GET(paste0(mnv_base,"models/",models$idObject[models$name == diag_name],"/"),
- "bioEntities/elements/?columns=id,name,type,references,elementId,complexId"),
+ "bioEntities/elements/?columns=id,name,type,references,elementId,complexId,bounds"),
flatten = F)
message("Fetching entrez ids...")
@@ -86,6 +86,15 @@ translated_sif <- raw_sif
### Retrieve Entrez for the entire columns of sources and targets
translated_sif[,1] <- sapply(raw_sif[,1], group_elements, model_elements, entrez)
translated_sif[,3] <- sapply(raw_sif[,3], group_elements, model_elements, entrez)
+### Collect x.y information
+colnames(translated_sif) <- c("source", "sign", "target")
+s.xy <- t(sapply(raw_sif[,1], function(x) unlist(model_elements$bounds[model_elements$elementId == x, c(3,4)])))
+colnames(s.xy) <- c("source.x", "source.y")
+t.xy <- t(sapply(raw_sif[,3], function(x) unlist(model_elements[model_elements$elementId == x,1][,c(3,4)])))
+colnames(t.xy) <- c("targets.x", "targets.y")
+### Combine into a single data frame
+translated_sif <- data.frame(translated_sif, s.xy, t.xy)
+
write.table(translated_sif, file = "translated_sif.txt",
sep = "\t", quote = F, col.names = F, row.names = F)
-message("Done.")
\ No newline at end of file
+message("Done.")
--
GitLab