Mercurial > repos > ppericard > mixomics_blocksplsda
diff mixomics_blocksplsda_script.R @ 1:6595c17673cb draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
| author | ppericard |
|---|---|
| date | Wed, 12 Jun 2019 11:22:33 -0400 |
| parents | bea08702ed51 |
| children | 0a3c83f2197a |
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--- a/mixomics_blocksplsda_script.R Fri May 17 05:00:22 2019 -0400 +++ b/mixomics_blocksplsda_script.R Wed Jun 12 11:22:33 2019 -0400 @@ -164,17 +164,17 @@ # print("Block.splsda variates:") # print(mixomics_result$variates) -for(bname in names(mixomics_result$variates)) +for(block_name in names(mixomics_result$variates)) { - # print(bname) - # print(mixomics_result$variates[[bname]]) + # print(block_name) + # print(mixomics_result$variates[[block_name]]) # Format the column names to add the block name and replace spaces - colnames(mixomics_result$variates[[bname]]) <- paste("block.splsda", bname, gsub(" ", "_", colnames(mixomics_result$variates[[bname]])), sep = "_") - # print(mixomics_result$variates[[bname]]) + colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_") + # print(mixomics_result$variates[[block_name]]) # Append the new columns to the sample metadata matrix - sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[bname]]) + sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]]) } # print(sample_metadata) @@ -196,6 +196,9 @@ meta_variable <- mixomics_result$loadings[[block_name]] # print(head(meta_variable)) + # Format the column names to add the block name and replace spaces + colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_") + # Read input block variable metadata files if provided (optional) if(block_meta_var != "None") {