Set mean as default

prabhakarlab · Feb 18, 2024 · cc791fe · cc791fe
1 parent 98bc6e0
commit cc791fe
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Banksy
 Title: Spatial transcriptomic clustering
-Version: 0.99.6
+Version: 0.99.7
 Authors@R: c(
     person(given = "Vipul",
            family = "Singhal",
@@ -19,7 +19,7 @@ Description: Banksy is an R package that incorporates spatial information to
     neighbor-augmented product space which can then be clustered, allowing for
     accurate and spatially-aware cell typing and tissue domain segmentation. 
 Depends:
-     R (>= 4.3.0)
+     R (>= 4.4.0)
 Imports:
     aricode,
     data.table,
@@ -41,7 +41,7 @@ License: file LICENSE
 Encoding: UTF-8
 URL: https://github.com/prabhakarlab/Banksy
 BugReports: https://github.com/prabhakarlab/Banksy/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     knitr,
     rmarkdown,

diff --git a/R/cluster.R b/R/cluster.R
@@ -81,7 +81,7 @@
 #' 
 clusterBanksy <-
     function(se,
-             use_agf = TRUE,
+             use_agf = FALSE,
              lambda = 0.2,
              use_pcs = TRUE, 
              npcs = 20L,

diff --git a/R/computation.R b/R/computation.R
@@ -68,7 +68,7 @@
 computeBanksy <- function(se,
                           assay_name,
                           coord_names = NULL,
-                          compute_agf = TRUE,
+                          compute_agf = FALSE,
                           k_geom = 15,
                           spatial_mode = c("kNN_median", "kNN_r", 
                                            "kNN_rn", "kNN_rank", "kNN_unif", 

diff --git a/R/reduction.R b/R/reduction.R
@@ -41,7 +41,7 @@
 #' spe <- runBanksyPCA(spe, M = 1, lambda = 0.2, npcs = 20)
 #'
 runBanksyPCA <- function(se,
-                         use_agf = TRUE,
+                         use_agf = FALSE,
                          lambda = 0.2,
                          npcs = 20L,
                          assay_name = NULL,
@@ -156,7 +156,7 @@ checkBanksyPCA <- function(params) {
 #' spe <- runBanksyUMAP(spe, M = 1, lambda = 0.2)
 #'
 runBanksyUMAP <- function(se,
-                          use_agf = TRUE,
+                          use_agf = FALSE,
                           lambda = 0.2,
                           use_pcs = TRUE,
                           npcs = 20L,

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/batch-correction.html b/docs/articles/batch-correction.html
diff --git a/docs/articles/domain-segment.html b/docs/articles/domain-segment.html
diff --git a/docs/articles/figures/batch-correction-spatial-1.png b/docs/articles/figures/batch-correction-spatial-1.png
diff --git a/docs/articles/figures/batch-correction-umap-1.png b/docs/articles/figures/batch-correction-umap-1.png
diff --git a/docs/articles/index.html b/docs/articles/index.html