Merge pull request #82 from stemangiola/generalise-to-0-dimensions

Generalise to 0 dimensions

Author: stemangiola

R/print_method.R

@@ -68,13 +68,15 @@ print.SummarizedExperiment <- function(x, ..., n=NULL,
   # Fix NOTEs
   . <- NULL
 
+
   # Stop if any column or row names are duplicated
   if (check_if_any_dimnames_duplicated(x, dim = "cols")) {
       stop("tidySummarizedExperiment says: some column names are duplicated")
   }
   if (check_if_any_dimnames_duplicated(x, dim = "rows")) {
       stop("tidySummarizedExperiment says: some row names are duplicated")
   }
+
   # Stop if column names of assays do not overlap
   if (check_if_assays_are_NOT_overlapped(x, dim = "cols")) { 
       stop( 
@@ -96,11 +98,12 @@ but they do not completely overlap."
     my_tibble <-
         x |>
 
-        # If I have more than 30 genes select first sample
-        when(
-            nrow(.) > 30 ~.[1:min(50, nrow(x)), min(1, ncol(x)), drop=FALSE],
-            ~ .[, 1:min(20, ncol(x)), drop=FALSE]
-        ) %>%
+    # If I have more than 30 genes select first sample
+    when(
+      nrow(.) > 30 ~.[1:min(50, nrow(x)), min(1, ncol(x)), drop=FALSE] ,
+      ncol(.) == 0 ~ .,
+      ~ .[, 1:min(20, ncol(x)), drop=FALSE]
+    ) %>%
 
         as_tibble() 
 

R/tidyr_methods.R

@@ -225,7 +225,7 @@ nest.SummarizedExperiment <- function(.data, ..., .names_sep=NULL) {
     # Check if the nesting is too complicated
     # for the moment without optimisation
     my_test_nest <- 
-        my_data__[1,1] %>%
+        my_data__[min(1, nrow(my_data__)),min(1, ncol(my_data__))] %>%
         as_tibble() %>%
         tidyr::nest(...) 
 
@@ -279,47 +279,44 @@ nest.SummarizedExperiment <- function(.data, ..., .names_sep=NULL) {
         as_tibble() %>%
         tidyr::nest(...) |> 
 
-        mutate(
+          mutate(
             !!as.symbol(col_name_data) := pmap(
 
-                # Add sample feature to map if nesting by those
+              # Add sample feature to map if nesting by those
                 list(!!as.symbol(col_name_data)) %>%
+
+                  # Check if nested by sample
+                  when(sample_name %in% colnames(my_test_nest) ~ c(., list(!!sample_symbol)), ~ (.)) %>%
+
+                  # Check if nested by feature
+                  when(feature_name %in% colnames(my_test_nest) ~ c(., list(!!feature_symbol)), ~ (.)) , ~ { 
+                    
+                    # VERY COMPLICATE WAY TO DO THIS. SIMPLIFY IN THE FUTURE
+                    
                     # Check if nested by sample
-                    when(sample_name %in% colnames(my_test_nest) ~
-                        c(., list(!!sample_symbol)), ~ (.)) %>%
+                    if(sample_name %in% colnames(my_test_nest)) { my_samples=..2 }
+                    
+                    # Here I am filtering because if I have 0 samples this leads to failure
+                    else my_samples= ..1 |> filter(!is.na(!!sample_symbol)) |> pull(!!sample_symbol)
 
-                    # Check if nested by feature
-                    when(feature_name %in% colnames(my_test_nest) ~
-                        c(., list(!!feature_symbol)), ~ (.)), ~ {
+                    # Check if nested by feature and sample
+                    if(sample_name %in% colnames(my_test_nest) & feature_name %in% colnames(my_test_nest)) {my_transcripts=..3}
+                    else if(feature_name %in% colnames(my_test_nest)) my_transcripts=..2
 
-                        # VERY COMPLICATE WAY TO DO THIS.
-                        # SIMPLIFY IN THE FUTURE
+                    # Here I am filtering because if I have 0 features this leads to failure
+                    else my_transcripts= ..1 |> filter(!is.na(!!feature_symbol)) |>  pull(!!feature_symbol)
 
-                        # Check if nested by sample
-                        if (sample_name %in% colnames(my_test_nest)) {
-                            my_samples=..2
-                        } else {
-                            my_samples=pull(..1,!!sample_symbol)
-                        }
-
-                        # Check if nested by feature and sample
-                        if (sample_name %in% colnames(my_test_nest) &
-                            feature_name %in% colnames(my_test_nest)) {
-                            my_transcripts=..3
-                        } else if (feature_name %in% colnames(my_test_nest)) {
-                            my_transcripts=..2  
-                        } else {
-                            my_transcripts=pull(..1,!!feature_symbol)                            
-                        }
-                        ###
-
-                        my_data__[unique(my_transcripts), unique(my_samples)] |>
-                            select(-one_of(
-                                my_nesting_column |> 
-                                setdiff(c(sample_name, feature_name))
-                            )) |> 
-                            suppressWarnings()    
-                    }
+                    ###
+
+                    my_data__[unique(my_transcripts),unique(my_samples)] |>
+                      select(-one_of(
+                        my_nesting_column |> 
+                          setdiff(c(sample_name, feature_name))
+                      )) |> 
+                      suppressWarnings()
+
+                 
+                }
             )
         ) %>%
         # Coerce to tidySummarizedExperiment_nested for unnesting