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changeset 0:bd35f3b66a1e draft

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
author azomics
date Mon, 22 Jun 2020 17:54:03 -0400
parents
children 33b8673272cf
files FlowSOMCompare.R FlowSOMCompare.xml test-data/count.tabular test-data/input1.fcs test-data/input2.fcs test-data/input3.fcs test-data/mean.tabular test-data/median.tabular test-data/out1.pdf test-data/out1.tabular test-data/out2.pdf test-data/out2.tabular test-data/prop.tabular test-data/reftree.fsom
diffstat 14 files changed, 1037 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FlowSOMCompare.R	Mon Jun 22 17:54:03 2020 -0400
@@ -0,0 +1,234 @@
+#!/usr/bin/Rscript
+# Module for Galaxy
+# Compares groups of FCS to FlowSOM reference tree
+# with FlowSOM
+######################################################################
+#                  Copyright (c) 2017 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+library(FlowSOM)
+library(flowCore)
+
+checkFiles <- function(groups){
+  all_files <- unlist(groups)
+  all_unique <- unique(all_files)
+  if (length(all_unique) != length(all_files)) {
+      quit(save = "no", status = 14, runLast = FALSE)
+  }
+}
+
+compareLists <- function(m1, m2){
+  listCheck <- T
+  if (is.na(all(m1==m2))) {
+    mm1 <- is.na(m1)
+    mm2 <- is.na(m2)
+    if (all(mm1==mm2)){
+      if (!all(m1==m2, na.rm=TRUE)){
+        listCheck <- F
+      }
+    } else {
+      listCheck <- F
+    }
+  } else if (!all(m1==m2)) {
+    listCheck <- F
+  }
+  return(listCheck)
+}
+
+prettyMarkerNames <- function(flowFrame){
+  n <- flowFrame@parameters@data[, "name"]
+  d <- flowFrame@parameters@data[, "desc"]
+  d[is.na(d)] <- n[is.na(d)]
+  prettyNames <- list()
+  if(any(grepl("#",d))){
+      # Support for hashtag notation:
+      # antibody#fluorochrome -> antibody (fluorochrome)
+      prettyNames <- gsub("#(.*)$"," (\\1)",d)
+  } else {
+      prettyNames <- paste(d, " <", n, ">", sep="")
+  }
+  return(prettyNames)
+}
+
+compareToTree <- function(fst, wilc_thresh=0.05, output="", plot="", stats,
+                          comp_groups, filenames) {
+  groupRes <- CountGroups(fst, groups=comp_groups, plot=FALSE)
+  pdf(plot, useDingbats=FALSE, onefile=TRUE)
+  tresh <- wilc_thresh
+  pg <- PlotGroups(fst, groupRes, p_tresh=tresh)
+  dev.off()
+
+  nb_nodes <- length(pg[[1]])
+  nb_comp <- length(pg)
+  m <- matrix(0, nrow=nb_nodes, ncol=nb_comp+1)
+  s <- seq_len(nb_nodes)
+  m[,1]<- as.character(s)
+  for (i in 1:nb_comp){
+    m[s,i+1]<- as.character(pg[[i]])
+  }
+  groupnames <- attr(comp_groups,"names")
+  out_colnames <- paste(groupnames, collapse="-")
+  colnames(m) <- c("Node",out_colnames)
+  write.table(m, file=output, quote=F, row.names=F, col.names=T, sep='\t',
+              append=F)
+
+  ## get filenames
+  filepaths <- unlist(comp_groups)
+  fnames <- unlist(filenames)
+  nb_files <- length(filepaths)
+  comp_files <- list()
+  for (i in 1:length(filepaths)){
+    comp_files[[filepaths[[i]]]] <- fnames[[i]]
+  }
+
+  group_list <- list()
+  for (grp in attr(comp_groups, "names")) {
+    for (f in comp_groups[[grp]]){
+      group_list[[f]] <- grp
+    }
+  }
+  out_stats <- attr(stats, "names")
+  if ("counts" %in% out_stats){
+    gp_counts <- as.matrix(groupRes$counts)
+    tpc <- matrix("", nrow=nb_files, ncol=2)
+    tpc[,1] <- as.character(lapply(rownames(gp_counts), function(x) comp_files[[x]]))
+    tpc[,2] <- as.character(lapply(rownames(gp_counts), function(x) group_list[[x]]))
+    gp_counts <- cbind(tpc, gp_counts)
+    colnames(gp_counts)[[1]] <- "Filename"
+    colnames(gp_counts)[[2]] <- "Group"
+    t_gp_counts <- t(gp_counts)
+    write.table(t_gp_counts, file=stats[["counts"]], quote=F, row.names=T, col.names=F, sep='\t',
+                append=F)
+  }
+  if ("pctgs" %in% out_stats){
+    gp_prop <- as.matrix(groupRes$pctgs)
+    tpp <- matrix("", nrow=nb_files, ncol=2)
+    tpp[,1] <- as.character(lapply(rownames(gp_prop), function(x) comp_files[[x]]))
+    tpp[,2] <- as.character(lapply(rownames(gp_prop), function(x) group_list[[x]]))
+    gp_prop <- cbind(tpp, gp_prop)
+    colnames(gp_prop)[[1]] <- "Filename"
+    colnames(gp_prop)[[2]] <- "Group"
+    t_gp_prop <- t(gp_prop)
+    write.table(t_gp_prop, file=stats[["pctgs"]], quote=F, row.names=T, col.names=F, sep='\t',
+                append=F)
+  }
+  if ("means" %in% out_stats){
+    gp_mean <- as.matrix(groupRes$means)
+    t_gp_mean <- t(gp_mean)
+    tpm <- matrix(0, nrow=nb_nodes, ncol=1)
+    tpm[,1] <- seq_len(nb_nodes)
+    t_gp_mean <- cbind(tpm, t_gp_mean)
+    colnames(t_gp_mean)[[1]] <- "Nodes"
+    write.table(t_gp_mean, file=stats[["means"]], quote=F, row.names=F, col.names=T, sep='\t',
+                append=F)
+  }
+  if ("medians" %in% out_stats){
+    gp_med <- as.matrix(groupRes$medians)
+    t_gp_med <- t(gp_med)
+    tpd <- matrix(0, nrow=nb_nodes, ncol=1)
+    tpd[,1] <- seq_len(nb_nodes)
+    t_gp_med <- cbind(tpd, t_gp_med)
+    colnames(t_gp_med)[[1]] <- "Nodes"
+    write.table(t_gp_med, file=stats[["medians"]], quote=F, row.names=F, col.names=T, sep='\t',
+                append=F)
+  }
+}
+
+checkFCS <- function(tree, output="", plot="", thresh = 0.05, stats, groups,
+                     filenames) {
+
+  fcsfiles <- unlist(groups)
+  tree_valid <- F
+  markerCheck <- T
+  tryCatch({
+    fsomtree <- readRDS(tree)
+    tree_valid <- T
+  }, error = function(ex) {
+    print(paste(ex))
+  })
+
+  fst <- if (length(fsomtree)==2) fsomtree[[1]] else fsomtree
+
+  if (tree_valid){
+    tree_markers <- as.vector(fst$prettyColnames)
+    tree_channels <- as.vector(colnames(fst$data))
+    if (length(tree_markers) < 1){
+      quit(save = "no", status = 11, runLast = FALSE)
+    }
+  } else {
+    quit(save = "no", status = 11, runLast = FALSE)
+  }
+
+  for (i in 1:length(fcsfiles)){
+    is_file_valid <- F
+    tryCatch({
+      fcs <- read.FCS(fcsfiles[i], transformation=FALSE)
+      is_file_valid <- T
+    }, error = function(ex) {
+      print(paste(ex))
+    })
+    if (i == 1) {
+      m1 <- as.vector(pData(parameters(fcs))$desc)
+      c1 <- colnames(fcs)
+      # compare to tree markers
+      pm <- prettyMarkerNames(fcs)
+      if (!all(tree_markers %in% pm)){
+        quit(save = "no", status = 13, runLast = FALSE)
+      }
+    } else {
+      m2 <- as.vector(pData(parameters(fcs))$desc)
+      c2 <- colnames(fcs)
+      markerCheck <- compareLists(m1,m2)
+      markerChannel <- compareLists(c1,c2)
+    }
+  }
+  if (markerCheck && markerChannel) {
+    compareToTree(fst, thresh, output, plot, stats, groups, filenames)
+  } else {
+    quit(save = "no", status = 12, runLast = FALSE)
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+
+first_g1 <- 5
+tot_args <- length(args)
+g <- list()
+tmplist <- c("counts", "means", "medians", "pctgs")
+
+for (i in 5:13){
+  if (args[i] %in% tmplist){
+    first_g1 <- first_g1 + 2
+    g[[args[i]]] <- args[i+1]
+  }
+}
+
+tmpargs <- paste(args[first_g1:tot_args], collapse="=%=")
+tmpgroups <- strsplit(tmpargs, "=%=DONE=%=")
+
+groups <- list()
+filenames <- list()
+for (gps in tmpgroups[[1]]) {
+  tmpgroup <- strsplit(gps, "=%=")
+  nb_files <- (length(tmpgroup[[1]]) - 1 ) /2
+  tmplist <- character(nb_files)
+  tmpnames <- character(nb_files)
+  j <- 1
+  for (i in 2:length(tmpgroup[[1]])){
+    if (!i%%2){
+      tmplist[[j]] <- tmpgroup[[1]][i]
+      tmpnames[[j]]<- tmpgroup[[1]][i+1]
+      j <- j + 1
+    }
+  }
+  groups[[tmpgroup[[1]][1]]] <- tmplist
+  filenames[[tmpgroup[[1]][1]]] <- tmpnames
+}
+
+checkFiles(groups)
+checkFCS(args[1], args[2], args[3], args[4], g, groups, filenames)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FlowSOMCompare.xml	Mon Jun 22 17:54:03 2020 -0400
@@ -0,0 +1,195 @@
+<tool id="flowsom_compare" name="Compare Samples" version="1.0+galaxy1">
+  <description>using a FlowSOM tree</description>
+  <requirements>
+    <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="10" level="fatal" description="Please provide valid input FCS files." />
+    <exit_code range="11" level="fatal" description="Please provide a valid reference SOM tree." />
+    <exit_code range="12" level="fatal" description="There are inconsistencies in markers and/or channels between FCS files." />
+    <exit_code range="13" level="fatal" description="FCS file and reference tree markers and/or channels are inconsistent." />
+    <exit_code range="14" level="fatal" description="Some FCS files are used more than once." />
+  </stdio>
+  <command><![CDATA[
+    Rscript $__tool_directory__/FlowSOMCompare.R '${reftree}' '${groups}' '${plot}' '${thresh}'
+  #if $count == "TRUE"
+    'counts' '${count_out}'
+  #end if
+  #if $mean == "TRUE"
+    'means' '${mean_out}'
+  #end if
+  #if $med == "TRUE"
+    'medians' '${med_out}'
+  #end if
+  #if $prctg == "TRUE"
+    'pctgs' '${p_out}'
+  #end if
+    '${name1}'
+  #for $f in $group1
+    '${f}' '${f.name}'
+  #end for
+    'DONE' '${name2}'
+  #for $ff in $group2
+    '${ff}' '${ff.name}'
+  #end for
+  ]]>
+  </command>
+  <inputs>
+    <param format="fsom" name="reftree" type="data" label="FlowSOM Reference Tree"/>
+    <param name="name1" value="Group 1" type="text" label="Label for first group of files" help="This label will be used in the output tables."/>
+    <param format="fcs" name="group1" type="data_collection" collection_type="list" label="FCS files Collection"/>
+    <param name="name2" value="Group 2" type="text" label="Label for second group of files" help="This label will be used in the output tables."/>
+    <param format="fcs" name="group2" type="data_collection" collection_type="list" label="FCS files Collection"/>
+    <param name="thresh" type="float" value="0.05" label="Wilcox-test threshold for differential"  help="By default, the threshold is set to 0.05" />
+    <param name="count" type="boolean" label="Output counts of events in clusters for each file?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+    <param name="prctg" type="boolean" label="Output proportions of events in clusters for each file?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+    <param name="mean" type="boolean" label="Output means of proportions for each group?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+    <param name="med" type="boolean" label="Output medians of proportions for each group?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+  </inputs>
+  <outputs>
+    <data format="tabular" name="groups" label="Comparison of '${name1}' and '${name2}' to ${reftree.name}"/>
+    <data format="pdf" name="plot" label="Plot of comparison of '${name1}' and '${name2}' to ${reftree.name}"/>
+    <data format="tabular" name="count_out" label="Counts of events in samples of '${name1}' and '${name2}' in comparison to ${reftree.name}">
+      <filter>(count)</filter>
+    </data>
+    <data format="tabular" name="med_out" label="Median of proportions of event in '${name1}' and '${name2}' in comparison to ${reftree.name}">
+      <filter>(med)</filter>
+    </data>
+    <data format="tabular" name="mean_out" label="Means of proportions of events in '${name1}' and '${name2}' in comparison to ${reftree.name}">
+      <filter>(mean)</filter>
+    </data>
+    <data format="tabular" name="p_out" label="Proportions of events in samples of '${name1}' and '${name2}' in comparison to ${reftree.name}">
+      <filter>(prctg)</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="reftree" value="reftree.fsom"/>
+      <param name="name1" value="Group 1"/>
+      <param name="thresh" value="0.05"/>
+      <param name="group1">
+        <collection type="list">
+          <element name="input1.fcs" value="input1.fcs"/>
+        </collection>
+      </param>
+      <param name="name2" value="Group 2"/>
+      <param name="group2">
+        <collection type="list">
+          <element name="input2.fcs" value="input2.fcs"/>
+          <element name="input3.fcs" value="input3.fcs"/>
+        </collection>
+      </param>
+      <param name="count" value="FALSE"/>
+      <param name="mean" value="FALSE"/>
+      <param name="med" value="FALSE"/>
+      <param name="prctg" value="FALSE"/>
+      <output name="groups" file="out1.tabular" compare="sim_size"/>
+      <output name="plot" file="out1.pdf" compare="sim_size" delta="100000"/>
+    </test>
+    <test>
+      <param name="reftree" value="reftree.fsom"/>
+      <param name="name1" value="Group 1"/>
+      <param name="thresh" value="0.05"/>
+      <param name="group1">
+        <collection type="list">
+          <element name="input1.fcs" value="input1.fcs"/>
+        </collection>
+      </param>
+      <param name="name2" value="Group 2"/>
+      <param name="group2">
+        <collection type="list">
+          <element name="input2.fcs" value="input2.fcs"/>
+          <element name="input3.fcs" value="input3.fcs"/>
+        </collection>
+      </param>
+      <param name="count" value="TRUE"/>
+      <param name="mean" value="TRUE"/>
+      <param name="med" value="TRUE"/>
+      <param name="prctg" value="TRUE"/>
+      <output name="groups" file="out2.tabular" compare="sim_size"/>
+      <output name="plot" file="out2.pdf" compare="sim_size" delta="100000"/>
+      <output name="count_out" file="count.tabular" compare="sim_size"/>
+      <output name="mean_out" file="mean.tabular" compare="sim_size"/>
+      <output name="med_out" file="median.tabular" compare="sim_size"/>
+      <output name="p_out" file="prop.tabular" compare="sim_size"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+Compare sample
+-------------------
+
+This tool uses FlowSOM to compare two or more groups of files to a reference FlowSOM tree.
+
+**Input**
+
+This tool requires a reference FlowSOM tree, as well as two dataset collections of FCS files. Each group is compared to the reference tree. The statistical differential threshold is based on a Wilcox-test, with a p-value of 0.05 by default.
+
+.. class:: infomark
+
+If there is only one group to compare to the tree, the first set of FCS files should be the one used to generate the reference tree.
+
+**Output**
+
+This tool generates a table with groups attribution to each FlowSOM node, as well as a plot per comparison. Tables of counts, mean, median, proportion and normalized mean per node and files or groups are optionally produced.
+
+-----
+
+**Example**
+
+*Output* - Node Table::
+
+   Node Group1-Group2
+   1    group1
+   2    --
+   3    group2
+   4    group1
+   ...  ...
+
+*Output* - Counts of events in file per node Table::
+
+   Filename filename1 filename2 filename3 filename4 ...
+   Group    group1    group1    group2    group2    ...
+   1        17        2230      18        5054      ...
+   2        760       9         249       178       ...
+   3        155       9         1337      4         ...
+   4        53        2         1754      0         ...
+   5        42        1739      140       1320      ...
+   ...      ...       ...       ...       ...       ...
+
+*Output* - Proportion of events in file per node Table::
+
+   Filename filename1 filename2 filename3 filename4 ...
+   Group    group1    group1    group2    group2    ...
+   1        0.0002528 0.0346386 0.0003068 0.0905507 ...
+   2        0.0113029 0.0001397 0.0042441 0.0031891 ...
+   3        0.0023052 0.0001397 0.0227888 7.1666606 ...
+   4        0.0007882 3.1066030 0.0298965 0.00017   ...
+   5        0.0006246 0.0270119 0.0023862 0.2365714 ...
+   ...      ...       ...       ...       ...       ...
+
+*Output* - Means of proportions of events in group per node Table::
+
+   Nodes group1  group2
+   1     0.00025 0.01747
+   2     0.01130 0.00219
+   3     0.00230 0.01146
+   4     0.00078 0.01496
+   5     0.00062 0.01469
+   ...   ...     ...
+
+*Output* - Medians of proportions of events in group per node Table::
+
+   Nodes group1  group2
+   1     0.00025 0.01747
+   2     0.01130 0.00219
+   3     0.00230 0.01146
+   4     0.00078 0.01496
+   5     0.00062 0.01469
+   ...   ...     ...
+
+  ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1002/cyto.a.22625</citation>
+  </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count.tabular	Mon Jun 22 17:54:03 2020 -0400
@@ -0,0 +1,102 @@
+Filename	input1.fcs	input3.fcs	input2.fcs
+Group	Group 1	Group 2	Group 2
+1	620	1311	937
+2	674	790	795
+3	492	474	753
+4	49	179	79
+5	231	199	51
+6	528	402	39
+7	523	490	58
+8	465	528	93
+9	278	481	90
+10	206	402	53
+11	571	876	539
+12	952	555	539
+13	721	876	997
+14	731	192	248
+15	119	120	60
+16	88	1	78
+17	51	2	137
+18	49	6	177
+19	41	3	157
+20	153	392	140
+21	567	553	487
+22	825	497	467
+23	630	579	734
+24	368	195	382
+25	28	1	51
+26	29	1	79
+27	16	2	211
+28	16	0	294
+29	11	0	240
+30	169	158	151
+31	139	235	134
+32	475	246	295
+33	364	194	277
+34	65	58	191
+35	90	21	253
+36	14	0	75
+37	7	1	204
+38	2	0	134
+39	11	0	116
+40	184	20	27
+41	203	207	274
+42	111	183	183
+43	101	87	102
+44	45	107	105
+45	76	49	248
+46	28	17	149
+47	17	10	185
+48	11	1	157
+49	20	0	4
+50	202	2	2
+51	207	258	234
+52	202	212	246
+53	131	37	95
+54	255	142	192
+55	36	13	44
+56	18	13	78
+57	41	43	93
+58	98	0	4
+59	154	1	1
+60	687	8	4
+61	168	244	173
+62	85	252	202
+63	60	14	39
+64	45	16	80
+65	11	6	196
+66	3	9	271
+67	27	4	5
+68	111	1	3
+69	156	0	1
+70	528	4	0
+71	56	421	337
+72	23	417	347
+73	59	13	53
+74	15	1	62
+75	10	3	136
+76	1	1	294
+77	24	3	4
+78	442	1	1
+79	526	0	0
+80	788	1	2
+81	7	470	338
+82	0	302	228
+83	4	475	350
+84	4	471	387
+85	3	604	438
+86	0	382	287
+87	16	1	8
+88	205	1	0
+89	598	1	1
+90	712	0	0
+91	2	314	247
+92	0	381	312
+93	3	480	391
+94	5	612	465
+95	1	535	425
+96	0	624	414
+97	2	504	281
+98	122	0	0
+99	473	1	0
+100	510	1	0
Binary file test-data/input1.fcs has changed
Binary file test-data/input2.fcs has changed
Binary file test-data/input3.fcs has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mean.tabular	Mon Jun 22 17:54:03 2020 -0400
@@ -0,0 +1,101 @@
+Nodes	Group 1	Group 2
+1	0.031	0.0562
+2	0.0337	0.039625
+3	0.0246	0.030675
+4	0.00245	0.00645
+5	0.01155	0.00625
+6	0.0264	0.011025
+7	0.02615	0.0137
+8	0.02325	0.015525
+9	0.0139	0.014275
+10	0.0103	0.011375
+11	0.02855	0.035375
+12	0.0476	0.02735
+13	0.03605	0.046825
+14	0.03655	0.011
+15	0.00595	0.0045
+16	0.0044	0.001975
+17	0.00255	0.003475
+18	0.00245	0.004575
+19	0.00205	0.004
+20	0.00765	0.0133
+21	0.02835	0.026
+22	0.04125	0.0241
+23	0.0315	0.032825
+24	0.0184	0.014425
+25	0.0014	0.0013
+26	0.00145	0.002
+27	8e-04	0.005325
+28	8e-04	0.00735
+29	0.00055	0.006
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+99	0.02365	2.5e-05
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/median.tabular	Mon Jun 22 17:54:03 2020 -0400
@@ -0,0 +1,101 @@
+Nodes	Group 1	Group 2
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Binary file test-data/out1.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out1.tabular	Mon Jun 22 17:54:03 2020 -0400
@@ -0,0 +1,101 @@
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Binary file test-data/out2.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out2.tabular	Mon Jun 22 17:54:03 2020 -0400
@@ -0,0 +1,101 @@
+Node	Group 1-Group 2
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/prop.tabular	Mon Jun 22 17:54:03 2020 -0400
@@ -0,0 +1,102 @@
+Filename	input1.fcs	input3.fcs	input2.fcs
+Group	Group 1	Group 2	Group 2
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+16	0.0044	5e-05	0.0039
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Binary file test-data/reftree.fsom has changed