From 38d496b773cb50a93c8b4d6b929ac80b355a7cd6 Mon Sep 17 00:00:00 2001 From: Ryan Routsong Date: Thu, 16 Jan 2025 12:24:14 -0600 Subject: [PATCH 1/2] feat: include resolution 0.1 in umaps --- workflow/scripts/seuratCiteSampleQC.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/scripts/seuratCiteSampleQC.R b/workflow/scripts/seuratCiteSampleQC.R index 0984433..1da99b7 100644 --- a/workflow/scripts/seuratCiteSampleQC.R +++ b/workflow/scripts/seuratCiteSampleQC.R @@ -341,7 +341,7 @@ seur <- RunUMAP(seur, reduction = 'pca', dims = 1:30, assay = 'RNA') coord <- Embeddings(seur, reduction='pca')[,1:30] d <- dist(coord, method="euclidean") -for(resolution in c(seq(0.2,1.0,0.2), 1.5, 2.0)){ +for(resolution in c(0.1, seq(0.2,1.0,0.2), 1.5, 2.0)){ seur <- FindClusters(seur, resolution = resolution) #Calculate silhouette scores and generate plots From db7af512b5bd3a53afe40be74bef57376526fdf6 Mon Sep 17 00:00:00 2001 From: Ryan Routsong Date: Thu, 16 Jan 2025 12:54:12 -0600 Subject: [PATCH 2/2] feat: add resolution 0.1 to non-cite workflow --- workflow/scripts/seuratSampleQC.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/scripts/seuratSampleQC.R b/workflow/scripts/seuratSampleQC.R index 5414a52..9e2b64d 100644 --- a/workflow/scripts/seuratSampleQC.R +++ b/workflow/scripts/seuratSampleQC.R @@ -201,7 +201,7 @@ seur <- RunUMAP(seur, reduction = 'pca', dims = 1:30, assay = 'RNA') coord <- Embeddings(seur, reduction='pca')[,1:30] d <- dist(coord, method="euclidean") -for(resolution in c(seq(0.2,1.0,0.2), 1.5, 2.0)){ +for(resolution in c(0.1, seq(0.2,1.0,0.2), 1.5, 2.0)){ seur <- FindClusters(seur, resolution = resolution) #Calculate silhouette scores and generate plots