From 88922fb8d01104778a82229a1f9078febd17ba0d Mon Sep 17 00:00:00 2001
From: hrehrauer <Hubert.Rehrauer@fgcz.uzh.ch>
Date: Wed, 9 Nov 2022 16:18:23 +0100
Subject: [PATCH] clean up report

---
 inst/templates/ScSeurat.Rmd | 33 ++++++++++++++++++---------------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/inst/templates/ScSeurat.Rmd b/inst/templates/ScSeurat.Rmd
index 315d8cfae..b9ea6a676 100644
--- a/inst/templates/ScSeurat.Rmd
+++ b/inst/templates/ScSeurat.Rmd
@@ -45,17 +45,16 @@ library(Seurat)
 library(AUCell)
 library(ezRun)
 library(HDF5Array)
+library(enrichR)
 knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE, knitr.table.format = "html")
-```
 
-```{r}
 clusterInfoFile <- "clusterInfos.xlsx"
 posMarkers <- readxl::read_xlsx("posMarkers.xlsx")
 scData <- readRDS("scData.rds")
 output <- readRDS("output.rds")
 scData$qc.doublet <- scData$doubletClass %in% "doublet"
 allCellsMeta <- readRDS("allCellsMeta.rds")
-param = readRDS("param.rds")
+param <- readRDS("param.rds")
 species <- getSpecies(param$refBuild)
 if (file.exists("singler.results.rds")){
   singler.results <- readRDS("singler.results.rds")
@@ -233,7 +232,8 @@ cellIdents_perSample <- data.frame(ident = Idents(scData), Sample=scData$Sample)
 barplot = ggplot(data=cellIdents_perSample, aes(x=ident, fill=Sample)) + geom_bar(stat="Count")
 barplot + labs(x="Cluster", y = "Number of cells", fill = "Sample")
 
-cells_prop = cellsProportion(scData, groupVar1 = "ident", groupVar2 = "Sample")
+
+cells_prop = cellsProportion(scData, groupVar1 = "seurat_clusters", groupVar2 = "Sample")
 kable(cells_prop,row.names=FALSE, format="html",caption="Cell proportions") %>% kable_styling(bootstrap_options = "striped", full_width = F, position = "float_right")
 ```
 
@@ -293,7 +293,9 @@ FeaturePlot(scData, features="negLog10CellPValue", label = TRUE)
 ```{r, fig.width=12, fig.height=shrinkToRange(length(param$controlSeqs)*3/4, c(6, 18)), eval=ezIsSpecified(param$controlSeqs)}
 genesToPlot <- gsub("_", "-", param$controlSeqs)
 genesToPlot <- intersect(genesToPlot, rownames(scData))
-FeaturePlot(scData, genesToPlot) + NoLegend()
+if (length(genesToPlot) > 0){
+  FeaturePlot(scData, genesToPlot) + NoLegend()
+}
 ```
 
 #### Cluster resolution 
@@ -369,27 +371,28 @@ enrichrCalls <- paste0("<a href='javascript:void(0)' onClick='", jsCall,
 ```
 
 
-```{r load enrichR terms, echo=FALSE, results='asis', eval= !is.null(enrichRout)}
-enrichRTerm <- as.data.frame(do.call(rbind, lapply(enrichRout, as.vector)))
-enrichRTerm <- map_df(enrichRTerm, ~ map_df(.x, ~ replace(.x, is.null(.x), NA)), .id = "database")
-enrichRTerm <- enrichRTerm %>%
-  group_by(., Cluster, database) %>%
-  summarise(topTerms = paste(Term, collapse = "; ")) %>%
-  as.data.frame()
-enrichRTerm <- dcast(enrichRTerm, ... ~ database)
-enrichrTable <- merge(enrichrTable, enrichRTerm, by = "Cluster")
-```
 
 ```{r enrichr markers, echo=FALSE, results='asis'}
 enrichrTable <- tibble(Cluster=names(genesPerCluster),
                          "# of posMarkers"=lengths(genesPerCluster),
                          "Enrichr link"=enrichrCalls)
+if (!is.null(enrichRout)){
+  enrichRTerm <- as.data.frame(do.call(rbind, lapply(enrichRout, as.vector)))
+  enrichRTerm <- map_df(enrichRTerm, ~ map_df(.x, ~ replace(.x, is.null(.x), NA)), .id = "database")
+  enrichRTerm <- enrichRTerm %>%
+    group_by(., Cluster, database) %>%
+    summarise(topTerms = paste(Term, collapse = "; ")) %>%
+    as.data.frame()
+  enrichRTerm <- dcast(enrichRTerm, ... ~ database)
+  enrichrTable <- merge(enrichrTable, enrichRTerm, by = "Cluster")
+}
 kable(enrichrTable, format="html", escape=FALSE,
         caption=paste0("GeneSet enrichment")) %>%
 kable_styling("striped", full_width = F, position = "left")
 ```
 
 
+
 ```{r plot enrichR per cluster, fig.height=5, fig.width=10, eval= !is.null(enrichRout)}
 for (cluster in names(enrichRout)) {
   enrichRDataFrame <- as.data.frame(do.call(rbind, enrichRout[[cluster]]))