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feat: retain common samples on pgx multiomics upload #1620

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Merged
merged 1 commit into from
Nov 11, 2025
Merged

feat: retain common samples on pgx multiomics upload #1620

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12 changes: 12 additions & 0 deletions components/board.upload/R/upload_module_preview_counts.R
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Original file line number Diff line number Diff line change
Expand Up @@ -385,6 +385,7 @@ upload_table_preview_counts_server <- function(id,
}

# Load data once and cache both data frames and column names
samples_cache <- list()
data_cache <- list()
col_lists <- list()
file_names <- character()
Expand All @@ -403,6 +404,7 @@ upload_table_preview_counts_server <- function(id,
} else {
df <- pgx_data$counts
}
samples_cache[[i]] <- pgx_data$samples
data_cache[[i]] <- df
col_lists[[i]] <- colnames(df)
file_names[i] <- dataset
Expand Down Expand Up @@ -481,6 +483,16 @@ upload_table_preview_counts_server <- function(id,
df <- df[, common_cols, drop = FALSE]
combined_df <- rbind(combined_df, df)
}

# Combine samples_cache by intersecting rownames (only for pgx multi-omics upload)
if (length(samples_cache) > 0) {
# Find common rownames in all sample files (no prefixing!)
rownames_list <- lapply(samples_cache, rownames)
common_rows <- Reduce(intersect, rownames_list)
combined_samples <- samples_cache[[1]][common_rows, , drop = FALSE]
uploaded$samples.csv <- combined_samples
}

uploaded$counts.csv <- combined_df
})

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