diff --git a/episodes/cell_type_annotation.Rmd b/episodes/cell_type_annotation.Rmd index 5922bbc..024c506 100644 --- a/episodes/cell_type_annotation.Rmd +++ b/episodes/cell_type_annotation.Rmd @@ -530,13 +530,15 @@ estimate of the distribution. :::: challenge -The diagnostics don't look so good for some of the examples here. Which ones? Why? +Inspect the diagnostics for the next nine cell types. Do they look okay? ::: solution +```{r} +par(mfrow = c(3,3)) -The example that jumps out most strongly to the eye is ExE endoderm, which doesn't show clear separate modes. Simultaneously, Endothelium seems to have three or four modes. +AUCell_exploreThresholds(cell.aucs[10:18], plotHist = TRUE, assign = TRUE) +``` -Remember, this is an exploratory diagnostic, not the final word! At this point it'd be good to engage in some critical inspection of the results. Maybe we don't have enough / the best marker genes. In this particular case, the fact that we subsetted the reference set to 1000 cells probably didn't help. ::: :::: @@ -631,7 +633,8 @@ Generally, it's good to keep in mind that the concept of "everything else" is no :::: challenge -#### Extension Challenge 2z +#### Extension Challenge 2: Parallelizing SingleR + SingleR can be computationally expensive. How do you set it to run in parallel? ::: solution @@ -656,6 +659,21 @@ res2 <- SingleR(test = sce.mat, :::: +:::: challenge + +#### Extension Challenge 3: Critical inspection of diagnostics + +The first set of AUCell diagnostics don't look so good for some of the examples here. Which ones? Why? + +::: solution + +The example that jumps out most strongly to the eye is ExE endoderm, which doesn't show clear separate modes. Simultaneously, Endothelium seems to have three or four modes. + +Remember, this is an exploratory diagnostic, not the final word! At this point it'd be good to engage in some critical inspection of the results. Maybe we don't have enough / the best marker genes. In this particular case, the fact that we subsetted the reference set to 1000 cells probably didn't help. +::: + +:::: + ::: checklist ## Further Reading