From dba5e1e2521566bb8900267df535083a42a0e722 Mon Sep 17 00:00:00 2001 From: dimalvovs Date: Sat, 31 Aug 2024 15:58:39 -0400 Subject: [PATCH] change list accession approach dure to nf var substitution --- modules/local/spacemarkers.nf | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/modules/local/spacemarkers.nf b/modules/local/spacemarkers.nf index 51c1a0e..93fb6c1 100644 --- a/modules/local/spacemarkers.nf +++ b/modules/local/spacemarkers.nf @@ -88,29 +88,31 @@ process SPACEMARKERS_MQC { #!/usr/bin/env Rscript dir.create("${prefix}", showWarnings = FALSE) + #[['']] notation needed to allow nextflow var susbtitution + sm <- readRDS("$spaceMarkers") - smi <- sm[which(sapply(sm, function(x) length(x$interacting_genes))>0)] + smi <- sm[which(sapply(sm, function(x) length(x[['interacting_genes']]))>0)] #interacting patterns stats - n_pairs_total <- length(sm$pattern) + n_pairs_total <- length(sm) n_pairs_interact <- length(smi) #spacemarker metric max_spacemarker_metric <- max(sapply(smi, function(x) { - max(x$interacting_genes[[1]]$SpaceMarkersMetric) + max(x[['interacting_genes']][[1]][['SpaceMarkersMetric']]) })) min_spacemarker_metric <- min(sapply(smi, function(x) { - min(x$interacting_genes[[1]]$SpaceMarkersMetric) + min(x[['interacting_genes']][[1]][['SpaceMarkersMetric']]) })) #average number of genes in each pair avg_genes_in_pair <- mean(sapply(smi, function(x) { - length(x$interacting_genes[[1]]$Gene) + length(x[['interacting_genes']][[1]][['Gene']]) })) - #average percent overlap across patterns + #average percent overlap across interacting patterns avg_hot_share_in_pair <- mean(sapply(smi, function(x) { - sum(!is.na(x$hotspots))/length(x$hotspots[,1]) + sum(!is.na(x[['hotspots']]))/length(x[['hotspots']][,1]) })) #report