Improve documentation

NAMESPACE

@@ -135,9 +135,11 @@ importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
 importFrom(stats,setNames)
 importFrom(stringr,regex)
+importFrom(stringr,str_c)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_remove)
 importFrom(stringr,str_replace_all)
+importFrom(stringr,str_subset)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
 importFrom(tibble,glimpse)

R/methods.R

@@ -33,6 +33,8 @@ setClass("tidySingleCellExperiment", contains="SingleCellExperiment")
 #' @importFrom dplyr contains
 #' @importFrom dplyr everything
 #' @importFrom ttservice join_features
+#' @importFrom stringr str_c
+#' @importFrom stringr str_subset
 #' @export
 setMethod("join_features", "SingleCellExperiment", function(.data,
     features=NULL, all=FALSE, exclude_zeros=FALSE, shape="long", ...) {
@@ -42,16 +44,40 @@ setMethod("join_features", "SingleCellExperiment", function(.data,
 
     # Shape is long
     if (shape == "long") {
-        .data %>%
-        left_join(
-            by=c_(.data)$name,
-            get_abundance_sc_long(
-                .data=.data,
-                features=features,
-                all=all,
-                exclude_zeros=exclude_zeros)) %>%
-        select(!!c_(.data)$symbol, .feature,
-            contains(".abundance"), everything())
+
+        # Suppress generic data frame creation message produced by left_join
+        suppressMessages({
+            .data <-
+                .data %>%
+                    left_join(
+                        by=c_(.data)$name,
+                        get_abundance_sc_long(
+                            .data=.data,
+                            features=features,
+                            all=all,
+                            exclude_zeros=exclude_zeros)) %>%
+                    select(!!c_(.data)$symbol, .feature,
+                        contains(".abundance"), everything())
+        })
+
+        # Provide data frame creation and abundance column message
+        if (any(class(.data) == "tbl_df")) {
+
+            abundance_columns <-
+                .data %>%
+                colnames() %>%
+                stringr::str_subset('.abundance_')
+
+            message(stringr::str_c("tidySingleCellExperiment says: join_features produces",
+                " duplicate cell names to accomadate the long data format. For this reason, a data", 
+                " frame is returned for independent data analysis. Assay feature abundance is", 
+                " appended as ", 
+                stringr::str_flatten_comma(abundance_columns, last = " and "), "."
+            ))
+        }
+
+        .data
+
     # Shape if wide
     } else {
         .data  %>%

README.Rmd

@@ -97,6 +97,19 @@ pbmc_small_tidy
 assay(pbmc_small_tidy, "counts")[1:5, 1:5]
 ```
 
+The `SingleCellExperiment` object's tibble visualisation can be turned off, or back on at any time.
+
+```{r}
+# Turn off the tibble visualisation
+options("restore_SingleCellExperiment_show" = TRUE)
+pbmc_small_tidy
+```
+
+```{r}
+# Turn on the tibble visualisation
+options("restore_SingleCellExperiment_show" = FALSE)
+```
+
 # Annotation polishing
 
 We may have a column that contains the directory each run was taken from, such as the "file" column in `pbmc_small_tidy`.

README.md

@@ -98,7 +98,7 @@ pbmc_small_tidy
 ```
 
     ## # A SingleCellExperiment-tibble abstraction: 80 × 17
-    ## # Features=230 | Cells=80 | Assays=counts, logcounts
+    ## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
     ##    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
     ##    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
     ##  1 ATGC… SeuratPro…         70           47 0               A             g2    
@@ -135,6 +135,29 @@ assay(pbmc_small_tidy, "counts")[1:5, 1:5]
     ## CD79A                .
     ## HLA-DRA              1
     ## TCL1A                .
+
+The `SingleCellExperiment` object's tibble visualisation can be turned off, or back on at any time.
+
+```{r}
+# Turn off the tibble visualisation
+options("restore_SingleCellExperiment_show" = TRUE)
+pbmc_small_tidy
+```
+
+    ## class: SingleCellExperiment 
+    ## dim: 230 80 
+    ## metadata(0):
+    ## assays(2): counts logcounts
+    ## rownames(230): MS4A1 CD79B ... SPON2 S100B
+    ## rowData names(5): vst.mean vst.variance vst.variance.expected
+    ##   vst.variance.standardized vst.variable
+    ## colnames(80): ATGCCAGAACGACT CATGGCCTGTGCAT ... GGAACACTTCAGAC CTTGATTGATCTTC
+    ## colData names(9): orig.ident nCount_RNA ... file ident
+
+```{r}
+# Turn on the tibble visualisation
+options("restore_SingleCellExperiment_show" = FALSE)
+```
 
 # Annotation polishing
 
@@ -167,7 +190,7 @@ pbmc_small_polished |>
 ```
 
     ## # A SingleCellExperiment-tibble abstraction: 80 × 18
-    ## # Features=230 | Cells=80 | Assays=counts, logcounts
+    ## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
     ##    .cell sample orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
     ##    <chr> <chr>  <fct>           <dbl>        <int> <fct>           <fct>        
     ##  1 ATGC… sampl… SeuratPro…         70           47 0               A            
@@ -294,7 +317,7 @@ pbmc_small_pca
 ```
 
     ## # A SingleCellExperiment-tibble abstraction: 80 × 18
-    ## # Features=230 | Cells=80 | Assays=counts, logcounts
+    ## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
     ##    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
     ##    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
     ##  1 ATGC… SeuratPro…         70           47 0               A             g2    
@@ -356,7 +379,7 @@ pbmc_small_cluster |> select(label, everything())
 ```
 
     ## # A SingleCellExperiment-tibble abstraction: 80 × 19
-    ## # Features=230 | Cells=80 | Assays=counts, logcounts
+    ## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
     ##    .cell  label orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
     ##    <chr>  <fct> <fct>           <dbl>        <int> <fct>           <fct>        
     ##  1 ATGCC… 2     SeuratPro…         70           47 0               A            
@@ -509,7 +532,7 @@ pbmc_small_cell_type |>
     ## your workflow to reflect the new vocabulary (.cell)
 
     ## # A SingleCellExperiment-tibble abstraction: 80 × 23
-    ## # Features=230 | Cells=80 | Assays=counts, logcounts
+    ## # [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m
     ##    cell          first.labels orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8
     ##    <chr>         <chr>        <fct>           <dbl>        <int> <fct>          
     ##  1 ATGCCAGAACGA… CD4+ T-cells SeuratPro…         70           47 0              

vignettes/introduction.Rmd

@@ -93,6 +93,18 @@ pbmc_small_tidy
 counts(pbmc_small_tidy)[1:5, 1:4]
 ```
 
+The `SingleCellExperiment` object's tibble visualisation can be turned off, or back on at any time.
+
+```{r}
+# Turn off the tibble visualisation
+options("restore_SingleCellExperiment_show" = TRUE)
+pbmc_small_tidy
+```
+```{r}
+# Turn on the tibble visualisation
+options("restore_SingleCellExperiment_show" = FALSE)
+```
+
 # Annotation polishing
 
 We may have a column that contains the directory each run was taken from,