bugfixes

SydneyBioX · Oct 22, 2024 · 83440e8 · 83440e8
1 parent c1940ac
commit 83440e8
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/.gitignore b/.gitignore
@@ -16,3 +16,5 @@ Meta
 .vscode
 debug
 docs
+/doc/
+/Meta/
diff --git a/R/spicy.R b/R/spicy.R
@@ -167,6 +167,10 @@ spicy <- function(cells,
 
   spicyResult = list()
 
+
+  comparisons <- data.frame(from = m1,
+                            to = m2,
+                            labels = labels)
 
   ## Find pairwise associations
 
@@ -185,16 +189,13 @@ spicy <- function(cells,
     )
     pairwiseAssoc <- as.data.frame(pairwiseAssoc)
     pairwiseAssoc <- pairwiseAssoc[labels]
+
   }
 
 
   if (!is.null(alternateResult)) {
     pairwiseAssoc <- alternateResult
 
-    comparisons <- data.frame(from = m1,
-                              to = m2,
-                              labels = labels)
-
     # Checking if Kontextual result.
     if (isTRUE(attr(alternateResult, "kontextualResult"))) {
       pairwiseAssoc <- alternateResult

diff --git a/vignettes/spicyR.Rmd b/vignettes/spicyR.Rmd
@@ -62,9 +62,8 @@ library(ggplot2)
 library(SpatialExperiment)
 library(SpatialDatasets)
 library(imcRtools)
-library(tidyverse)
+library(dplyr)
 library(survival)
-library(ggsurvfit)
 ```
-Original file line number
+Diff line change
@@ Expand Up / @@ -16,3 +16,5 @@ Meta @@
     .vscode
     debug
     docs
+    /doc/
+    /Meta/