adds pkgs and fixes color

sib-swiss · Jun 11, 2024 · ca22792 · ca22792
1 parent 9be11fb
commit ca22792
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Showing 3 changed files with 25 additions and 2 deletions.
diff --git a/3_integration_clustering.qmd b/3_integration_clustering.qmd
@@ -52,7 +52,8 @@ seu_int <- IntegrateData(anchors, normalization.method = "SCT")
 seu_int <- FindVariableFeatures(seu_int)
 seu_int <- RunPCA(seu_int, npcs = 50, verbose = FALSE)
 seu_int <- RunUMAP(seu_int, reduction = "pca", dims = 1:50)
-DimPlot(seu_int, reduction = "umap")
+DimPlot(seu_int, reduction = "umap") + 
+  scale_color_viridis_d(option = "cividis")
 ```
 
 

diff --git a/renv.lock b/renv.lock
@@ -1491,6 +1491,26 @@
       ],
       "Hash": "80f374ef8500fcdc5d84a0345b837227"
     },
+    "downlit": {
+      "Package": "downlit",
+      "Version": "0.4.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "brio",
+        "desc",
+        "digest",
+        "evaluate",
+        "fansi",
+        "memoise",
+        "rlang",
+        "vctrs",
+        "withr",
+        "yaml"
+      ],
+      "Hash": "45a6a596bf0108ee1ff16a040a2df897"
+    },
     "downloader": {
       "Package": "downloader",
       "Version": "0.4",

diff --git a/scripts/deps.R b/scripts/deps.R
@@ -3,4 +3,6 @@ library(bit)
 library(bit64)
 library(glmGamPoi)
 library(Rfast2)
-library(presto)
+library(presto)
+library(downlit)
+library(xml2)