Merge pull request #45 from ccb-hms/hca_refresh

hca_refresh question titles

episodes/hca.Rmd

@@ -110,7 +110,7 @@ metadata |>
   glimpse()
 ```
 
-## A note on the piping operator
+## A note on the pipe operator
 
 The vignette materials provided by `CuratedAtlasQueryR` show the use of the
 'native' R pipe (implemented after R version `4.1.0`). For those not familiar
@@ -182,9 +182,9 @@ For the sake of demonstration, we'll focus this small subset of samples:
 sample_subset = metadata |>
     filter(
         ethnicity == "African" &
-        stringr::str_like(assay, "%10x%") &
+        grepl("10x", assay) &
         tissue == "lung parenchyma" &
-        stringr::str_like(cell_type, "%CD4%")
+        grepl("CD4", cell_type)
     )
 ```
 
@@ -246,7 +246,7 @@ single_cell_counts |> saveHDF5SummarizedExperiment("single_cell_counts")
 
 :::::::::::::::::::::::::::::::::: challenge
 
-#### Exercise 1
+#### Exercise 1: Basic counting + piping
 
 Use `count` and `arrange` to get the number of cells per tissue in descending
 order.
@@ -264,26 +264,28 @@ metadata |>
 
 :::::::::::::::::::::::::::::::::: challenge
 
-#### Exercise 2
+#### Exercise 2: Tissue & type counting
 
-Use `dplyr`-isms to group by `tissue` and `cell_type` and get a tally of the
-highest number of cell types per tissue combination. What tissue has the most
-numerous type of cells? 
+`count()` can group by multiple factors by simply adding another grouping column
+as an additional argument. Get a tally of the highest number of cell types per
+tissue combination. What tissue has the most numerous type of cells?
 
 :::::::::::::: solution
 
 ```{r,eval=FALSE}
 metadata |>
     count(tissue, cell_type) |>
-    arrange(-n)
+    arrange(-n) |> 
+    head(n = 1)
+
 ```
 :::::::::::::::::::::::
 
 :::::::::::::::::::::::::::::::::::::::::::::
 
 :::::::::::::::::::::::::::::::::: challenge
 
-#### Exercise 3
+#### Exercise 3: Comparing metadata categories
 
 Spot some differences between the `tissue` and `tissue_harmonised` columns.
 Use `count` to summarise.
@@ -299,6 +301,10 @@ metadata |>
     count(tissue_harmonised) |>
     arrange(-n)
 ```
+
+For example you can see that `tissue_harmonised` merges the `cortex of kidney`
+and `kidney` groups in `tissue`.
+
 To see the full list of curated columns in the metadata, see the Details section
 in the `?get_metadata` documentation page.
 
@@ -308,7 +314,7 @@ in the `?get_metadata` documentation page.
 
 :::::::::::::::::::::::::::::::::: challenge
 
-#### Exercise 4
+#### Exercise 4: Highly specific cell groups
 
 Now that we are a little familiar with navigating the metadata, let's obtain
 a `SingleCellExperiment` of 10X scRNA-seq counts of `cd8 tem` `lung` cells for
@@ -322,13 +328,15 @@ metadata |>
     filter(
         sex == "female" &
         age_days > 80 * 365 &
-        stringr::str_like(assay, "%10x%") &
+        grepl("10x", assay) &
         disease == "COVID-19" &  
         tissue_harmonised == "lung" & 
         cell_type_harmonised == "cd8 tem"
     ) |>
     get_single_cell_experiment()
 ```
+
+You can see we don't get very many cells given the strict set of conditions we used.
 :::::::::::::::::::::::
 
 :::::::::::::::::::::::::::::::::::::::::::::