only map over relevant sample ids, and knit updated notebook

AlexsLemonade · Nov 1, 2024 · 79ceef2 · 79ceef2
1 parent 742e77e
commit 79ceef2
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diff --git a/...s/cell-type-wilms-tumor-06/notebook/07_combined_annotation_across_samples_exploration.Rmd b/...s/cell-type-wilms-tumor-06/notebook/07_combined_annotation_across_samples_exploration.Rmd
@@ -119,9 +119,13 @@ the following information per cell:
 sample_metadata_file <- file.path(repository_base, "data", "current", "SCPCP000006", "single_cell_metadata.tsv")
 
 metadata <- read.table(sample_metadata_file, sep = "\t", header = TRUE)
+sample_ids <- metadata |>
+  dplyr::filter(seq_unit != "spot") |>
+  dplyr::pull(scpca_sample_id) |>
+  unique()
 
 # Create a data frames of all annotations
-cell_type_df <- unique(metadata$scpca_sample_id) |>
+cell_type_df <- sample_ids |>
   purrr::map(
     # For each sample_id, do the following:
     \(sample_id) {