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comparison Seurat.R @ 9:c4db6ec33fec draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"
author iuc
date Thu, 21 Oct 2021 15:57:20 +0000
parents 764f076e9d52
children fab6ff46e019
comparison
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8:828324f3292f 9:c4db6ec33fec
113 #+ echo = FALSE 113 #+ echo = FALSE
114 if (showcode == TRUE && heatmaps == TRUE) print("Marker Genes") 114 if (showcode == TRUE && heatmaps == TRUE) print("Marker Genes")
115 #+ echo = `showcode`, warning = `warn`, include = `heatmaps` 115 #+ echo = `showcode`, warning = `warn`, include = `heatmaps`
116 markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold) 116 markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold)
117 top10 <- dplyr::group_by(markers, cluster) 117 top10 <- dplyr::group_by(markers, cluster)
118 top10 <- dplyr::top_n(top10, 10, avg_logFC) 118 top10 <- dplyr::top_n(top10, 10, avg_log2FC)
119 Seurat::DoHeatmap(seuset, features = top10$gene) 119 Seurat::DoHeatmap(seuset, features = top10$gene)
120 # nolint end 120 # nolint end