Merge pull request #35 from jackbibby1/v1.5.1

V1.5.1
jackbibby1 · Feb 7, 2023 · e0ea6ee · e0ea6ee
2 parents 5e31362 + 28a0d2f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: SCPA
 Title: Single Cell Pathway Analysis
-Version: 1.5.0
+Version: 1.5.1
 Authors@R: 
     c(person("Jack", "Bibby", , "jack.bibby@nih.gov", role = c("aut", "cre")),
       person("Divyansh", "Agarwal", role = c("aut")))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+## SCPA v1.5.1
+
+### Minor changes
+
+Fix downsample so it isn't forcing 500 cells [#34](https://github.com/jackbibby1/SCPA/issues/34)
+
 ## SCPA v1.5.0
 
 #### Major changes
@@ -7,6 +13,10 @@ and `compare_sce()` functions. Users just
 need to specify `parallel = TRUE` and `cores = x` to use parallel processing instead of calling
 `compare_pathways_parallel()`
 
+#### Minor changes
+
+- Fix downsample [#31](https://github.com/jackbibby1/SCPA/pull/31/commits/da5b7bf3a11abbf071ca5e2a9c5743a3a9f320fb)
+
 ## SCPA v1.4.0
 
 #### Major changes

diff --git a/R/ComparePathways.R b/R/ComparePathways.R
@@ -1,4 +1,4 @@
-#' Use SCPA to compare gene sets
+#' Internal function for compare_pathways()
 #'
 #' This function takes an input of samples and pathways
 #' to compare gene set perturbations over different conditions with SCPA.
@@ -164,7 +164,7 @@ single_comparison <- function(samples,
 
 }
 
-#' Use SCPA to compare gene sets
+#' Internal function for compare_pathways()
 #'
 #' This function takes an input of samples and pathways
 #' to compare gene set perturbations over different conditions with SCPA.
@@ -381,15 +381,15 @@ compare_pathways <- function(samples,
 
     mcm_output <- single_comparison(samples,
                                  pathways,
-                                 downsample = 500,
+                                 downsample = downsample,
                                  min_genes = 15,
                                  max_genes = 500)
 
   } else {
 
     mcm_output <- parallel_comparison(samples,
                                   pathways,
-                                  downsample = 500,
+                                  downsample = downsample,
                                   min_genes = 15,
                                   max_genes = 500,
                                   cores = cores)

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/comparing_two_populations.html b/docs/articles/comparing_two_populations.html
diff --git a/docs/articles/disease_comparison.html b/docs/articles/disease_comparison.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/interpreting_scpa_output.html b/docs/articles/interpreting_scpa_output.html
diff --git a/docs/articles/parallel_implementation.html b/docs/articles/parallel_implementation.html
diff --git a/docs/articles/pseudotime.html b/docs/articles/pseudotime.html
diff --git a/docs/articles/quick_start.html b/docs/articles/quick_start.html
diff --git a/docs/articles/seurat_comparison.html b/docs/articles/seurat_comparison.html