Mercurial > repos > bgruening > music_manipulate_eset
annotate scripts/dendrogram.R @ 3:192355cd1641 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50
author | bgruening |
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date | Tue, 29 Oct 2024 13:39:12 +0000 |
parents | 22232092be53 |
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22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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1 ## |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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2 suppressWarnings(suppressPackageStartupMessages(library(xbioc))) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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3 suppressWarnings(suppressPackageStartupMessages(library(MuSiC))) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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4 suppressWarnings(suppressPackageStartupMessages(library(reshape2))) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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5 suppressWarnings(suppressPackageStartupMessages(library(cowplot))) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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6 ## We use this script to generate a clustering dendrogram of cell |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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7 ## types, using the prior labelling from scRNA. |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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8 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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9 read_list <- function(lfile) { |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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10 if (lfile == "None") { |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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11 return(NULL) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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12 } |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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13 return(read.table(file = lfile, header = FALSE, check.names = FALSE, |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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14 stringsAsFactors = FALSE)$V1) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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15 } |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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16 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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17 args <- commandArgs(trailingOnly = TRUE) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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18 source(args[1]) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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19 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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20 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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21 ## Perform the estimation |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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22 ## Produce the first step information |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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23 sub.basis <- music_basis(scrna_eset, clusters = celltypes_label, |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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24 samples = samples_label, |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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25 select.ct = celltypes) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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26 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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27 ## Plot the dendrogram of design matrix and cross-subject mean of |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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28 ## realtive abundance |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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29 ## Hierarchical clustering using Complete Linkage |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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30 d1 <- dist(t(log(sub.basis$Disgn.mtx + 1e-6)), method = "euclidean") |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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31 hc1 <- hclust(d1, method = "complete") |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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32 ## Hierarchical clustering using Complete Linkage |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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33 d2 <- dist(t(log(sub.basis$M.theta + 1e-8)), method = "euclidean") |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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34 hc2 <- hclust(d2, method = "complete") |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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35 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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36 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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37 if (length(data.to.use) > 0) { |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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38 ## We then perform bulk tissue cell type estimation with pre-grouping |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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39 ## of cell types: C, list_of_cell_types, marker genes name, marker |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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40 ## genes list. |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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41 ## data.to.use = list( |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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42 ## "C1" = list(cell.types = c("Neutro"), |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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43 ## marker.names=NULL, |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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44 ## marker.list=NULL), |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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45 ## "C2" = list(cell.types = c("Podo"), |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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46 ## marker.names=NULL, |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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47 ## marker.list=NULL), |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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48 ## "C3" = list(cell.types = c("Endo","CD-PC","LOH","CD-IC","DCT","PT"), |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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49 ## marker.names = "Epithelial", |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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50 ## marker.list = read_list("../test-data/epith.markers")), |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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51 ## "C4" = list(cell.types = c("Macro","Fib","B lymph","NK","T lymph"), |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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52 ## marker.names = "Immune", |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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53 ## marker.list = read_list("../test-data/immune.markers")) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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54 ## ) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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55 grouped_celltypes <- lapply(data.to.use, function(x) { |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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56 x$cell.types |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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57 }) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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58 marker_groups <- lapply(data.to.use, function(x) { |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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59 x$marker.list |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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60 }) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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61 names(marker_groups) <- names(data.to.use) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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62 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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63 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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64 cl_type <- as.character(scrna_eset[[celltypes_label]]) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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65 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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66 for (cl in seq_len(length(grouped_celltypes))) { |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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67 cl_type[cl_type %in% |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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68 grouped_celltypes[[cl]]] <- names(grouped_celltypes)[cl] |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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69 } |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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70 pData(scrna_eset)[[clustertype_label]] <- factor( |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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71 cl_type, levels = c(names(grouped_celltypes), |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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72 "CD-Trans", "Novel1", "Novel2")) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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73 |
22232092be53
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74 est_bulk <- music_prop.cluster( |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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75 bulk.eset = bulk_eset, sc.eset = scrna_eset, |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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76 group.markers = marker_groups, clusters = celltypes_label, |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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77 groups = clustertype_label, samples = samples_label, |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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78 clusters.type = grouped_celltypes |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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79 ) |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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80 |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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81 estimated_music_props <- est_bulk$Est.prop.weighted.cluster |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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82 ## NNLS is not calculated here |
22232092be53
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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83 |
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84 ## Show different in estimation methods |
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85 ## Jitter plot of estimated cell type proportions |
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86 methods_list <- c("MuSiC") |
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87 |
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88 jitter_fig <- Jitter_Est( |
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89 list(data.matrix(estimated_music_props)), |
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90 method.name = methods_list, title = "Jitter plot of Est Proportions", |
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91 size = 2, alpha = 0.7) + |
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92 theme_minimal() + |
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93 labs(x = element_blank(), y = element_blank()) + |
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94 theme(axis.text = element_text(size = 6), |
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95 axis.text.x = element_blank(), |
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96 legend.position = "none") |
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97 |
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98 plot_box <- Boxplot_Est(list( |
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99 data.matrix(estimated_music_props)), |
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100 method.name = methods_list) + |
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101 theme_minimal() + |
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102 labs(x = element_blank(), y = element_blank()) + |
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103 theme(axis.text = element_text(size = 6), |
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104 axis.text.x = element_blank(), |
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105 legend.position = "none") |
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106 |
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107 plot_hmap <- Prop_heat_Est(list( |
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108 data.matrix(estimated_music_props)), |
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109 method.name = methods_list) + |
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110 labs(x = element_blank(), y = element_blank()) + |
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111 theme(axis.text.y = element_text(size = 6), |
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112 axis.text.x = element_text(angle = -90, size = 5), |
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113 plot.title = element_text(size = 9), |
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114 legend.key.width = unit(0.15, "cm"), |
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115 legend.text = element_text(size = 5), |
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116 legend.title = element_text(size = 5)) |
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117 |
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118 } |
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119 |
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120 pdf(file = outfile_pdf, width = 8, height = 8) |
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121 par(mfrow = c(1, 2)) |
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122 plot(hc1, cex = 0.6, hang = -1, main = "Cluster log(Design Matrix)") |
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123 plot(hc2, cex = 0.6, hang = -1, main = "Cluster log(Mean of RA)") |
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124 if (length(data.to.use) > 0) { |
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125 plot_grid(jitter_fig, plot_box, plot_hmap, ncol = 2, nrow = 2) |
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126 } |
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127 message(dev.off()) |
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128 |
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129 if (length(data.to.use) > 0) { |
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130 write.table(estimated_music_props, |
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131 file = outfile_tab, quote = F, col.names = NA, sep = "\t") |
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132 } |