install

Author: mjoppich

DESCRIPTION

@@ -11,8 +11,7 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.2
 Depends: R (>= 4.0.0)
-Imports: Tempora,
-            Seurat,
+Imports:    Seurat,
             ggplot2,
             cowplot,
             stringr,
@@ -24,7 +23,6 @@ Imports: Tempora,
             data.table,
             writexl,
             EnhancedVolcano,
-            ggsunburst,
             ggrepel,
             RColorBrewer,
             svglite,
@@ -36,7 +34,6 @@ Imports: Tempora,
             circlize,
             pbapply,
             future,
-            magritt,
             org.Mm.eg.db,
             org.Hs.eg.db,
             ReactomePA

LICENSE

@@ -433,7 +433,7 @@ comparativeVioBoxPlot = function( obj.sc, feature, group.by, adj.pval.threshold=
 
   if (!is.null(split.by))
   {
-    stat.test = rstatix::pairwise_t_test(stat.test,
+    stat.test = rstatix::pairwise_t_test(as.data.frame(stat.test),
         as.formula(paste(feature, " ~ ", split.by, sep="")), paired = FALSE, 
         p.adjust.method = "BH"
       )
@@ -442,7 +442,7 @@ comparativeVioBoxPlot = function( obj.sc, feature, group.by, adj.pval.threshold=
     print(head(as.data.frame(stat.test)))
 
 
-    stat.test = rstatix::pairwise_t_test(stat.test,
+    stat.test = rstatix::pairwise_t_test(as.data.frame(stat.test),
         as.formula(paste(feature, " ~ ", group.by, sep="")), paired = FALSE, 
         p.adjust.method = "BH"
       )

R/plots.R

@@ -58,7 +58,6 @@ finalList = prepareIntegration(objlist, cc.use.genes = cc.genes, nfeatures.varia
 
 integratedList_sample = performIntegration(finalList$data, "libintegration", features.integration = finalList$features, gex.method.normalization="LogNormalize", gex.method.integration="rpca", add.do=FALSE, run.parallel=FALSE)
 
-
 ```
 
 ```{r}
@@ -118,7 +117,6 @@ annotateList.sample_condition = list(
   list(name="TP 2", selector="^20094_0008"),
   list(name="TP 3", selector="^20094_0009"),
   list(name="Ctrl", selector="^20094_0012")
-
 )
 
 obj.integrated = annotateByCellnamePattern( obj.integrated, "tp", annotateList.sample_condition, order=c("Ctrl", "TP 1", "TP 2", "TP 3"))