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annotate FlowSOMCompare.R @ 1:33b8673272cf draft default tip

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planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
author azomics
date Fri, 29 Sep 2023 07:19:42 +0000
parents bd35f3b66a1e
children
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33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
azomics
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diff changeset
1 #!/usr/bin/env Rscript
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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2 # Module for Galaxy
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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3 # Compares groups of FCS to FlowSOM reference tree
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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4 # with FlowSOM
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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5 ######################################################################
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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6 # Copyright (c) 2017 Northrop Grumman.
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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7 # All rights reserved.
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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8 ######################################################################
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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9 #
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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10 # Version 1
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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11 # Cristel Thomas
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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12 #
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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13 #
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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14 library(FlowSOM)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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15 library(flowCore)
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16
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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17 check_files <- function(groups) {
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18 all_files <- unlist(groups)
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19 all_unique <- unique(all_files)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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20 if (length(all_unique) != length(all_files)) {
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33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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21 quit(save = "no", status = 14, runLast = FALSE)
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22 }
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23 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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24
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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25 compare_lists <- function(m1, m2) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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26 list_check <- TRUE
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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27 if (is.na(all(m1 == m2))) {
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28 mm1 <- is.na(m1)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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29 mm2 <- is.na(m2)
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33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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30 if (all(mm1 == mm2)) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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31 if (!all(m1 == m2, na.rm = TRUE)) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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32 list_check <- FALSE
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33 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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34 } else {
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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35 list_check <- FALSE
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36 }
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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37 } else if (!all(m1 == m2)) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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38 list_check <- FALSE
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39 }
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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40 return(list_check)
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41 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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42
1
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43 pretty_marker_names <- function(flow_frame) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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44 n <- flow_frame@parameters@data[, "name"]
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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45 d <- flow_frame@parameters@data[, "desc"]
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46 d[is.na(d)] <- n[is.na(d)]
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47 pretty_names <- list()
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48 if (any(grepl("#", d))) {
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49 # Support for hashtag notation:
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50 pretty_names <- gsub("#(.*)$", " (\\1)", d)
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51 } else {
1
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52 pretty_names <- paste(d, " <", n, ">", sep = "")
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53 }
1
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54 return(pretty_names)
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55 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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56
1
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57 compare_to_tree <- function(fst,
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58 wilc_thresh = 0.05, output = "", plot = "", stats,
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59 comp_groups, filenames) {
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60 group_res <- CountGroups(fst, groups = comp_groups, plot = FALSE)
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61 pdf(plot, useDingbats = FALSE, onefile = TRUE)
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62 tresh <- wilc_thresh
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63 pg <- PlotGroups(fst, group_res, p_tresh = tresh)
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64 dev.off()
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65
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66 nb_nodes <- length(pg[[1]])
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67 nb_comp <- length(pg)
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68 m <- matrix(0, nrow = nb_nodes, ncol = nb_comp + 1)
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69 s <- seq_len(nb_nodes)
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70 m[, 1] <- as.character(s)
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71 for (i in 1:nb_comp) {
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72 m[s, i + 1] <- as.character(pg[[i]])
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73 }
1
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74 groupnames <- attr(comp_groups, "names")
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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75 out_colnames <- paste(groupnames, collapse = "-")
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76 colnames(m) <- c("Node", out_colnames)
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77 write.table(m, file = output, quote = FALSE, row.names = FALSE,
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78 col.names = TRUE, sep = "\t",
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79 append = FALSE)
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80
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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81 ## get filenames
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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82 filepaths <- unlist(comp_groups)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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83 fnames <- unlist(filenames)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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84 nb_files <- length(filepaths)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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diff changeset
85 comp_files <- list()
1
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86 for (i in seq_along(filepaths)) {
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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87 comp_files[[filepaths[[i]]]] <- fnames[[i]]
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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88 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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89
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff changeset
90 group_list <- list()
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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91 for (grp in attr(comp_groups, "names")) {
1
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92 for (f in comp_groups[[grp]]) {
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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93 group_list[[f]] <- grp
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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94 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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diff changeset
95 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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96 out_stats <- attr(stats, "names")
1
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97 if ("counts" %in% out_stats) {
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98 gp_counts <- as.matrix(group_res$counts)
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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99 tpc <- matrix("", nrow = nb_files, ncol = 2)
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100 tpc[, 1] <- as.character(
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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101 lapply(rownames(gp_counts),
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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102 function(x) comp_files[[x]]))
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103 tpc[, 2] <- as.character(
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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104 lapply(rownames(gp_counts),
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105 function(x) group_list[[x]]))
0
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106 gp_counts <- cbind(tpc, gp_counts)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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107 colnames(gp_counts)[[1]] <- "Filename"
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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108 colnames(gp_counts)[[2]] <- "Group"
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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109 t_gp_counts <- t(gp_counts)
1
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110 write.table(t_gp_counts,
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111 file = stats[["counts"]],
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112 quote = FALSE,
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113 row.names = TRUE,
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114 col.names = FALSE,
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115 sep = "\t",
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116 append = FALSE)
0
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117 }
1
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118 if ("pctgs" %in% out_stats) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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119 gp_prop <- as.matrix(group_res$pctgs)
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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120 tpp <- matrix("", nrow = nb_files, ncol = 2)
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121 tpp[, 1] <- as.character(
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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122 lapply(rownames(gp_prop),
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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123 function(x) comp_files[[x]]))
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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124 tpp[, 2] <- as.character(
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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125 lapply(rownames(gp_prop),
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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126 function(x) group_list[[x]]))
0
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127 gp_prop <- cbind(tpp, gp_prop)
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128 colnames(gp_prop)[[1]] <- "Filename"
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129 colnames(gp_prop)[[2]] <- "Group"
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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130 t_gp_prop <- t(gp_prop)
1
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131 write.table(t_gp_prop,
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132 file = stats[["pctgs"]],
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133 quote = FALSE,
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134 row.names = TRUE,
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135 col.names = FALSE,
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136 sep = "\t",
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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137 append = FALSE)
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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138 }
1
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139 if ("means" %in% out_stats) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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140 gp_mean <- as.matrix(group_res$means)
0
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141 t_gp_mean <- t(gp_mean)
1
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142 tpm <- matrix(0, nrow = nb_nodes, ncol = 1)
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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143 tpm[, 1] <- seq_len(nb_nodes)
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144 t_gp_mean <- cbind(tpm, t_gp_mean)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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145 colnames(t_gp_mean)[[1]] <- "Nodes"
1
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146 write.table(t_gp_mean,
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147 file = stats[["means"]],
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148 quote = FALSE,
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149 row.names = FALSE,
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150 col.names = TRUE,
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151 sep = "\t",
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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152 append = FALSE)
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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153 }
1
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154 if ("medians" %in% out_stats) {
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155 gp_med <- as.matrix(group_res$medians)
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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156 t_gp_med <- t(gp_med)
1
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157 tpd <- matrix(0, nrow = nb_nodes, ncol = 1)
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158 tpd[, 1] <- seq_len(nb_nodes)
0
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159 t_gp_med <- cbind(tpd, t_gp_med)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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160 colnames(t_gp_med)[[1]] <- "Nodes"
1
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161 write.table(t_gp_med,
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162 file = stats[["medians"]],
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163 quote = FALSE,
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164 row.names = FALSE,
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165 col.names = TRUE,
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166 sep = "\t",
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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167 append = FALSE)
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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168 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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169 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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170
1
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171 check_fcs <- function(tree,
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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172 output = "", plot = "", thresh = 0.05, stats, groups,
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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173 filenames) {
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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174
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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175 fcsfiles <- unlist(groups)
1
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176 tree_valid <- FALSE
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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177 marker_check <- TRUE
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bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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178 tryCatch({
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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179 fsomtree <- readRDS(tree)
1
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180 tree_valid <- TRUE
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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181 }, error = function(ex) {
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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182 print(paste(ex))
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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183 })
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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184
1
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185 fst <- if (length(fsomtree) == 2) fsomtree[[1]] else fsomtree
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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186
1
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187 if (tree_valid) {
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188 tree_markers <- as.vector(fst$prettyColnames)
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189 if (length(tree_markers) < 1) {
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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190 quit(save = "no", status = 11, runLast = FALSE)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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191 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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192 } else {
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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193 quit(save = "no", status = 11, runLast = FALSE)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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194 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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195
1
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196 for (i in seq_along(fcsfiles)) {
0
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197 tryCatch({
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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198 fcs <- read.FCS(fcsfiles[i], transformation = FALSE)
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199 }, error = function(ex) {
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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200 print(paste(ex))
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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201 })
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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202 if (i == 1) {
0
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203 m1 <- as.vector(pData(parameters(fcs))$desc)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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204 c1 <- colnames(fcs)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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205 # compare to tree markers
1
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206 pm <- pretty_marker_names(fcs)
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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207 if (!all(tree_markers %in% pm)) {
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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208 quit(save = "no", status = 13, runLast = FALSE)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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209 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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210 } else {
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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211 m2 <- as.vector(pData(parameters(fcs))$desc)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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212 c2 <- colnames(fcs)
1
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213 marker_check <- compare_lists(m1, m2)
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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214 marker_channel <- compare_lists(c1, c2)
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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215 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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216 }
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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diff changeset
217 if (marker_check && marker_channel) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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218 compare_to_tree(fst, thresh, output, plot, stats, groups, filenames)
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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219 } else {
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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220 quit(save = "no", status = 12, runLast = FALSE)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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221 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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222 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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223
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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224 args <- commandArgs(trailingOnly = TRUE)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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225
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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226 first_g1 <- 5
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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227 tot_args <- length(args)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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228 g <- list()
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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229 tmplist <- c("counts", "means", "medians", "pctgs")
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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230
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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diff changeset
231 for (i in 5:13) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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232 if (args[i] %in% tmplist) {
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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233 first_g1 <- first_g1 + 2
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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diff changeset
234 g[[args[i]]] <- args[i + 1]
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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235 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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diff changeset
236 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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237
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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diff changeset
238 tmpargs <- paste(args[first_g1:tot_args], collapse = "=%=")
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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diff changeset
239 tmpgroups <- strsplit(tmpargs, "=%=DONE=%=")
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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240
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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diff changeset
241 groups <- list()
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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diff changeset
242 filenames <- list()
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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243 for (gps in tmpgroups[[1]]) {
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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244 tmpgroup <- strsplit(gps, "=%=")
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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245 nb_files <- (length(tmpgroup[[1]]) - 1) / 2
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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246 tmplist <- character(nb_files)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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247 tmpnames <- character(nb_files)
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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248 j <- 1
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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249 for (i in 2:length(tmpgroup[[1]])) {
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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250 if (!i %% 2) {
0
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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251 tmplist[[j]] <- tmpgroup[[1]][i]
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33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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252 tmpnames[[j]] <- tmpgroup[[1]][i + 1]
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bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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253 j <- j + 1
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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254 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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255 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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256 groups[[tmpgroup[[1]][1]]] <- tmplist
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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257 filenames[[tmpgroup[[1]][1]]] <- tmpnames
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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258 }
bd35f3b66a1e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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259
1
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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260 check_files(groups)
33b8673272cf planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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261 check_fcs(args[1], args[2], args[3], args[4], g, groups, filenames)