add export of filtered normalized counts #6

epigen · Apr 5, 2024 · 66a1933 · 66a1933
1 parent efddf06
commit 66a1933
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diff --git a/workflow/rules/mixscape.smk b/workflow/rules/mixscape.smk
@@ -38,6 +38,7 @@ rule lda:
         lda_object = os.path.join(result_path,'{sample}','FILTERED_object.rds'),
         filtered_metadata = os.path.join(result_path,'{sample}','FILTERED_metadata.csv'),
         lda_data = os.path.join(result_path,'{sample}','LDA_data.csv'),
+        filtered_assay_data = os.path.join(result_path,'{sample}','FILTERED_{}_data.csv'.format(config["assay"]),
         filtered_prtb_data = os.path.join(result_path,'{sample}','FILTERED_PRTB_data.csv'),
         lda_plot = report(os.path.join(result_path,'{sample}','plots','LDA_UMAP.png'), 
                           caption="../report/lda_umap.rst", 

diff --git a/workflow/scripts/lda.R b/workflow/scripts/lda.R
@@ -15,6 +15,7 @@ lda_object_path <- snakemake@output[["lda_object"]]
 lda_plot_path <- snakemake@output[["lda_plot"]] 
 lda_data_path <- snakemake@output[["lda_data"]] 
 filtered_prtb_data_path <- snakemake@output[["filtered_prtb_data"]]
+filtered_assay_data_path <- snakemake@output[["filtered_assay_data"]]
 
 # parameters
 assay <- snakemake@config[["assay"]]
@@ -119,3 +120,6 @@ fwrite(as.data.frame(lda_data), file=file.path(lda_data_path), row.names=TRUE)
 
 # save matrix of PRTB values
 fwrite(as.data.frame(GetAssayData(object = sub, slot = "data", assay = "PRTB")), file=file.path(filtered_prtb_data_path), row.names=TRUE)
+
+# save matrix of assay values
+fwrite(as.data.frame(GetAssayData(object = sub, slot = "data", assay = assay)), file=file.path(filtered_assay_data_path), row.names=TRUE)