Mercurial > repos > immport-devteam > profile_cl
changeset 0:8547aedf1350 draft
Uploaded
| author | immport-devteam |
|---|---|
| date | Mon, 27 Feb 2017 13:03:19 -0500 |
| parents | |
| children | 62d8985a41e2 |
| files | profile_cl/getOntology.R profile_cl/profileCLs.py profile_cl/profileCLs.xml profile_cl/static/flowtools/css/flowCL.css profile_cl/static/flowtools/js/profileCLs.js profile_cl/static/images/flowtools/popprofiles.png profile_cl/static/images/flowtools/profileCL.png profile_cl/templates/profileCLs.template profile_cl/test-data/CLprofiles.txt profile_cl/test-data/flowcl_pop01.pdf profile_cl/test-data/flowcl_pop01.txt profile_cl/test-data/flowcl_pop03.pdf profile_cl/test-data/flowcl_pop03.txt profile_cl/test-data/input.flowscore profile_cl/test-data/out.html profile_cl/test-data/scores.txt |
| diffstat | 16 files changed, 707 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/getOntology.R Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,28 @@ +# Cell Ontology Module for Galaxy +# FlowCL +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Version 1 +# Cristel Thomas +# +# + +library(flowCL) +library(base) + +getOntology <- function(output_file, markers) { + res <- flowCL(markers, ResetArch = TRUE) + if (length(res) == 6) { + report <- capture.output(res$Table) + sink(output_file) + cat(report, sep = "\n") + sink() + } +} + +args <- commandArgs(trailingOnly = TRUE) +markers <- paste(args[3:length(args)], collapse="") +getOntology(args[2], markers)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/profileCLs.py Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,163 @@ +#!/usr/bin/env python + +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +from __future__ import print_function +import sys +import os +from argparse import ArgumentParser +from jinja2 import Environment, FileSystemLoader + +profile_key = { + "1": "-", + "2": "lo", + "3": "+", + "4": "hi" +} + + +def run_flowCL(phenotype, output_txt, output_pdf, tool): + run_command = " ". join(["Rscript --slave --vanilla", tool, "--args", output_txt, phenotype]) + os.system(run_command) + get_graph = " ".join(["mv flowCL_results/*.pdf", output_pdf]) + os.system(get_graph) + return + + +def generate_flowCL_query(list_markers, list_types): + if (len(list_markers) != len(list_types)): + return("pb with headers") + query = [] + # go through both lists, remove fsc/ssc + for i in range(1, len(list_markers)): + if not list_markers[i].startswith("FSC") and not list_markers[i].startswith("SSC"): + query.append(list_markers[i].upper()) + query.append(profile_key[list_types[i]]) + # return concatenated string + return("".join(query)) + + +def translate_profiles(input_file, tool_dir, output, html_dir): + os.mkdir(html_dir) + + tool = "/".join([tool_dir, "getOntology.R"]) + html_table = "".join([html_dir, "/CLprofiles.txt"]) + score_table = "".join(["cp ", input_file, " ", html_dir, "/scores.txt"]) + os.system(score_table) + + # read profile + with open(input_file, "r") as flock_profiles, open(html_table, "w") as out: + headers = flock_profiles.readline() + headers = headers.strip() + # get all headers except for last 2 (count + percentage) + markers = headers.split("\t")[:-2] + counter = 0 + + out.write("Population\tFlowCL Query\tNb Results\tLink to PDF\t") + out.write("Top Result Label\tTop Result Score\tTop Result CL\n") + queries = {} + # create marker query for each population + for lines in flock_profiles: + lines = lines.strip("\n") + pop_profile = lines.split("\t")[:-2] + flowcl_query = generate_flowCL_query(markers, pop_profile) + counter += 1 + nb_results = "0" + top_label = "no_match" + top_score = "NA" + top_CL = "NA" + pdf_link = "NA" + # check if query was run before + if flowcl_query not in queries: + # create filenames for results & graphs + txt = "".join(["flowcl_pop", str(counter).zfill(2), ".txt"]) + text_result = "/".join([html_dir, txt]) + graph = "".join(["flowcl_pop", str(counter).zfill(2), ".pdf"]) + graph_output = "/".join([html_dir, graph]) + # run flowCL for each marker profile + run_flowCL(flowcl_query, text_result, graph_output, tool) + + # test that text file exists if not results are all NAs: + if os.path.isfile(text_result): + with open(text_result, "r") as res: + for line in res: + if line.startswith("Score"): + data = line.split(") ") + top_score = data[2][:-2] + tot_results = len(data) - 2 + nb_results = str(tot_results) + if tot_results == 5: + if len(data[6].split("+")) > 1: + nb_results = "5+" + elif line.startswith("Cell ID"): + prep_link = line.split(") ")[1][:-2] + cl = prep_link.replace("_", ":") + link = "".join(['<a href="http://www.immport-labs.org/immport-ontology/public/home/home/', cl, '" target="_blank">']) + top_CL = "".join([link, prep_link, "</a>"]) + elif line.startswith("Cell Label"): + top_label = line.split(") ")[1][:-2] + pdf_link = "".join(['<a href="', graph, '" target="_blank">PDF</a>']) + tmpflowcl_query = "".join(['<a href="', txt, '" target="_blank">', flowcl_query, '</a>']) + + queries[flowcl_query] = { + "query": tmpflowcl_query, + "results": nb_results, + "pdf": pdf_link, + "label": top_label, + "score": top_score, + "CL": top_CL + } + # write query results to CLprofiles.txt + out.write("\t".join([pop_profile[0], + queries[flowcl_query]["query"], + queries[flowcl_query]["results"], + queries[flowcl_query]["pdf"], + queries[flowcl_query]["label"], + queries[flowcl_query]["score"], + queries[flowcl_query]["CL"]]) + "\n") + + env = Environment(loader=FileSystemLoader(tool_dir + "/templates")) + template = env.get_template("profileCLs.template") + + real_directory = html_dir.replace("/job_working_directory", "") + context = {'outputDirectory': real_directory} + overview = template.render(**context) + with open(output, "w") as outf: + outf.write(overview) + + +if __name__ == "__main__": + parser = ArgumentParser( + prog="getCLs_from_profile", + description="runs flowCL on a each population defined by FLOCK.") + + parser.add_argument( + '-i', + dest="input_file", + required=True, + help="File location for the profile.txt from FLOCK.") + + parser.add_argument( + '-o', + dest="output", + required=True, + help="Name of the output html file.") + + parser.add_argument( + '-d', + dest="html_dir", + required=True, + help="Path to html supporting directory.") + + parser.add_argument( + '-t', + dest="tool_dir", + required=True, + help="Path to the tool directory") + + args = parser.parse_args() + + translate_profiles(args.input_file, args.tool_dir, args.output, args.html_dir) + sys.exit(0)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/profileCLs.xml Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,116 @@ +<tool id="get_profiles_cell_ontology" name="Associate FLOCK populations" version="1.1"> + <description>with cell ontology</description> + <requirements> + <requirement type="package" version="2.8">jinja2</requirement> + <requirement type="package" version="3.3.0">r</requirement> + <requirement type="package" version="1.11.2">bioconductor-flowcl</requirement> + </requirements> + <stdio> + <exit_code range="2" level="fatal" description="There was a problem running flowCL. You might want to check your marker names - See stderr for more details." /> + <exit_code range="3:" level="fatal" description="See stderr for more details." /> + </stdio> + <command><![CDATA[ + python $__tool_directory__/profileCLs.py -i "${input}" -o "${html_file}" -d "${html_file.files_path}" -t $__tool_directory__ + ]]> + </command> + <inputs> + <param format="flowscore" name="input" type="data" label="Population score profiles from FLOCK"/> + </inputs> + <outputs> + <data format="html" name="html_file" label="Cell ontology of ${input.name}"> + </data> + </outputs> + <tests> + <test> + <param name="input" value="input.flowscore"/> + <output name="html_file" file="out.html"> + <extra_files type="file" name="CLprofiles.txt" value="CLprofiles.txt"/> + <extra_files type="file" name="flowCL_pop01.pdf" value="flowCL_pop01.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop01.txt" value="flowCL_pop01.txt"/> + <extra_files type="file" name="flowCL_pop03.pdf" value="flowCL_pop03.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop03.txt" value="flowCL_pop03.txt"/> + <extra_files type="file" name="flowCL_pop04.pdf" value="flowCL_pop04.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop04.txt" value="flowCL_pop04.txt"/> + <extra_files type="file" name="flowCL_pop05.pdf" value="flowCL_pop05.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop05.txt" value="flowCL_pop05.txt"/> + <extra_files type="file" name="flowCL_pop06.pdf" value="flowCL_pop06.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop06.txt" value="flowCL_pop06.txt"/> + <extra_files type="file" name="flowCL_pop07.pdf" value="flowCL_pop07.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop07.txt" value="flowCL_pop07.txt"/> + <extra_files type="file" name="flowCL_pop09.pdf" value="flowCL_pop09.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop09.txt" value="flowCL_pop09.txt"/> + <extra_files type="file" name="flowCL_pop11.pdf" value="flowCL_pop11.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop11.txt" value="flowCL_pop11.txt"/> + <extra_files type="file" name="flowCL_pop13.pdf" value="flowCL_pop13.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop13.txt" value="flowCL_pop13.txt"/> + <extra_files type="file" name="flowCL_pop14.pdf" value="flowCL_pop14.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop14.txt" value="flowCL_pop14.txt"/> + <extra_files type="file" name="flowCL_pop15.pdf" value="flowCL_pop15.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop15.txt" value="flowCL_pop15.txt"/> + <extra_files type="file" name="flowCL_pop16.pdf" value="flowCL_pop16.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop16.txt" value="flowCL_pop16.txt"/> + <extra_files type="file" name="flowCL_pop17.pdf" value="flowCL_pop17.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop17.txt" value="flowCL_pop17.txt"/> + <extra_files type="file" name="flowCL_pop19.pdf" value="flowCL_pop19.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop19.txt" value="flowCL_pop19.txt"/> + <extra_files type="file" name="flowCL_pop20.pdf" value="flowCL_pop20.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop20.txt" value="flowCL_pop20.txt"/> + <extra_files type="file" name="flowCL_pop22.pdf" value="flowCL_pop22.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop22.txt" value="flowCL_pop22.txt"/> + <extra_files type="file" name="flowCL_pop23.pdf" value="flowCL_pop23.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop23.txt" value="flowCL_pop23.txt"/> + <extra_files type="file" name="flowCL_pop25.pdf" value="flowCL_pop25.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_pop25.txt" value="flowCL_pop25.txt"/> + <extra_files type="file" name="scores.txt" value="scores.txt"/> + </output> + </test> + </tests> + <help><![CDATA[ + This tool uses flowCL to find a match for each of the populations defined by FLOCK. + +.. class:: warningmark + +here some sort of reminder that trusting data from a software might not be the best way to go necessarily, and that it would be wise oh so wise to still look at the data to make sure that the scores from FLOCK mean what you think they mean. + +----- + +**Input** + +This tool reads in the population score profiles from FLOCK. + +.. class:: warningmark + +**The marker names need to be in the cell ontology for this to work** + +**Output** + +The output is a page that allows visualization of the data. + +----- + +**Example** + +*Input* + +*Population profile file*:: + + Population_ID Marker1 Marker2 Marker3 Count Percentage + 1 1 3 2 3885 6.44 + 2 1 3 4 2774 4.62 + 3 2 2 3 2151 3.59 + 4 1 3 2 1207 2.01 + + +*Output* + +The CL terms hyperlink to their representation in the Immport Cell Ontology browser. The full flowCL run summary is accessible by clicking on the phenotype. + +.. image:: static/images/profileCL.png + +.. image:: static/flowtools/popprofiles.png + ]]> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu807</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/static/flowtools/css/flowCL.css Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,34 @@ +/* +** DataTables config +*/ +div.dt-buttons { + float: right; +} +th { + font-size:16px; + text-align: left; +} +body td { + max-width: 50px; + font-size: 14px; + overflow: hidden; + text-overflow: ellipsis; +} +.cltable thead { + display:none; +} +.cltable td { + max-width: 40px; + word-break: break-all; + word-wrap: break-word; +} +.firstcol { + width: 160px; +} +.smallcols { + width: 100px; +} +div.dataTables_wrapper { + width: 95%; + margin: 0 auto; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/static/flowtools/js/profileCLs.js Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,85 @@ +// Copyright (c) 2016 Northrop Grumman. +// All rights reserved. + +var cl_table = './CLprofiles.txt'; +var scores_table = './scores.txt'; + +var displayCLTable = function(){ + d3.text(cl_table, function(error, data){ + var clHdgs = [], + clHTML = '<table id="cltable" class="display compact" cellspacing="0" width="100%"/>', + clTableData = [], + clHeadings = []; + + if (error){ + alert("Problem retrieving data"); + return; + } + clHdgs = data.split("\n")[0].split("\t"); + data = d3.tsv.parse(data); + clTableData = $.extend(true, [], data); + + clHdgs.forEach(function(d,i){ + clHeadings.push({"data" : d, "title" : d}); + }); + + $('#clprofiles').html(clHTML); + var clTable = $('#cltable').DataTable({ + columns: clHeadings, + dom: '<"top"Bi>t<"bottom"lp><"clear">', + pageLength: 25, + order: [[ 0, "asc" ]], + data: clTableData, + buttons: [ + 'copy', 'pdfHtml5','csvHtml5' + ], + columnDefs: [ + { + targets: [0,2,3], + className: "smallcols" + }, + { + targets: 4, + className: "dt-body-left" + }, + { + targets: [5,6], + className: "firstcol" + }] + }); + }); +}; + +var displayScoresTable = function(){ + d3.text(scores_table, function(error, data){ + var scoreHTML = '<table id="scoretable" class="display compact" cellspacing="0" width="100%"/>', + scoreHdgs = [], + scoreTableData = [], + scoreHeadings = []; + if (error){ + alert("Problem retrieving data"); + return; + } + scoreHdgs = data.split("\n")[0].split("\t"); + data = d3.tsv.parse(data); + + $('#scores').html(scoreHTML); + + scoreTableData = $.extend(true, [], data); + + scoreHdgs.forEach(function(d,i){ + scoreHeadings.push({"data" : d, "title" : d}); + }); + + var scoreTable = $('#scoretable').DataTable({ + columns: scoreHeadings, + pageLength: 25, + order: [[ 0, "asc" ]], + dom: '<"top"Bi>t<"bottom"lp><"clear">', + data: scoreTableData, + buttons: [ + 'copy', 'pdfHtml5','csvHtml5' + ], + }); + }); +};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/templates/profileCLs.template Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,91 @@ +<!DOCTYPE html> +<html> +<head lang="en"> +<title>FLOCK Populations Ontology</title> +<meta charset="UTF-8"> +<meta HTTP-EQUIV="Pragma" CONTENT="no-cache"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<link rel="stylesheet" href="/static/flowtools/bootstrap/css/bootstrap.css"/> +<link rel="stylesheet" href="/static/flowtools/select2/select2.min.css"/> +<link rel="stylesheet" href="/static/flowtools/css/flowCL.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/datatables.min.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/Buttons-1.1.2/css/buttons.dataTables.min.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/Select-1.1.2/css/select.dataTables.min.css"/> +<script src="/static/flowtools/jquery-1.11.3.min.js" type="text/javascript"></script> +<script src="/static/flowtools/bootstrap/js/bootstrap.js" type="text/javascript"></script> +<script src="/static/flowtools/select2/select2.full.min.js" type="text/javascript"></script> +<script src="/static/flowtools/d3/d3.min.js" type="text/javascript"></script> +<script src="/static/flowtools/datatables/datatables.min.js" type="text/javascript"></script> +<script src="/static/flowtools/js/profileCLs.js" type="text/javascript"></script> + +<style> +#input{font-family:Calibri,Arial} +table.dataTable tbody td.dt-body-right { + text-align: right; +} +#div{padding:5px;width:150px;height:100px;text-align:center} +table{width:100%;border:0px solid;border-collapse:collapse;text-align:center;} +th{background-color:#3e6db0;color:#fff;padding:5px;text-align:center} +</style> +</head> + +<body> +<div class="container-fluid"> + <div class="row" style="padding-bottom:10px;min-height:500px;"> + <div class="col-md-12" > + <ul class="nav nav-tabs tabs-main"> + <li class="homeTab active" data-value="clprofiles"><a href="#clprofiles" data-toggle="tab">Populations Cell Ontologies</a></li> + <li class="homeTab" data-value="scores"><a href="#scores" data-toggle="tab">Populations Score Profiles</a></li> + </ul> + + <div class="tab-content"> + <div class="tab-pane active" id="clprofiles" style="min-height:500px;"> + <div class="row"> + <div id="clprof"/> + </div> + </div> + </div> + <div class="tab-pane" id="scores" style="height:800px;"> + <div class="row"> + <div id="clprof"/> + </div> + </div> + </div> + </div> + </div> +</div> + + +</div> +</div> + + +<script> +var clprofilesLoaded = false; +var scoresLoaded = false; + +$().ready(function() { + $(document).on('shown.bs.tab','a[data-toggle="tab"]', function(e) { + var tab = e.target.getAttribute("href"); + if (tab == '#clprofiles') { + if (clprofilesLoaded) { + return true; + } + clprofilesLoaded = true; + displayCLTable(); + } + if (tab == '#scores') { + if (scoresLoaded) { + return true; + } + scoresLoaded = true; + displayScoresTable(); + } + }); + + clprofilesLoaded = true; + displayCLTable(); +}); +</script> +</body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/test-data/CLprofiles.txt Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,4 @@ +Population FlowCL Query Nb Results Link to PDF Top Result Label Top Result Score Top Result CL +1 <a href="flowcl_pop01.txt" target="_blank">CD4+CCR3-CD8-CCR7-</a> 5+ <a href="flowcl_pop01.pdf" target="_blank">PDF</a> effector CD4-positive, alpha-beta T cell 0.167 <a href="http://www.immport-labs.org/immport-ontology/public/home/home/CL:0001044" target="_blank">CL_0001044</a> +2 <a href="flowcl_pop01.txt" target="_blank">CD4+CCR3-CD8-CCR7-</a> 5+ <a href="flowcl_pop01.pdf" target="_blank">PDF</a> effector CD4-positive, alpha-beta T cell 0.167 <a href="http://www.immport-labs.org/immport-ontology/public/home/home/CL:0001044" target="_blank">CL_0001044</a> +3 <a href="flowcl_pop03.txt" target="_blank">CD4+CCR3-CD8+CCR7lo</a> 5+ <a href="flowcl_pop03.pdf" target="_blank">PDF</a> mature CD8_alpha-negative CD11b-positive dendritic cell 2)" -0.357 <a href="http://www.immport-labs.org/immport-ontology/public/home/home/CL:0001003" target="_blank">CL_0001003</a>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/test-data/flowcl_pop01.txt Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,44 @@ + [,1] +Short marker names "CD4+CCR3-CD8-CCR7-" +Ontology marker names "CD4 molecule, C-C chemokine receptor type 3, T cell receptor" + "co-receptor CD8, C-C chemokine receptor type 7" +Experiment markers "CD4,CCR3,CD8,CCR7" +Ontology exper. names "CD4 molecule, C-C chemokine receptor type 3, T cell receptor" + "co-receptor CD8, C-C chemokine receptor type 7" +Successful Match? "No" +Marker ID "1) PR_000001004, PR_000025402, PR_000001203 2) PR_000001004," + "PR_000025402, PR_000001203 3) PR_000001004, PR_000025402," + "PR_000001203 4) PR_000001004, PR_000025402 5) PR_000001004," + "PR_000025402 + more" +Marker Label "1) CD4 molecule, T cell receptor co-receptor CD8, C-C chemokine" + "receptor type 7 2) CD4 molecule, T cell receptor co-receptor CD8, C-C" + "chemokine receptor type 7 3) CD4 molecule, T cell receptor" + "co-receptor CD8, C-C chemokine receptor type 7 4) CD4 molecule, T" + "cell receptor co-receptor CD8 5) CD4 molecule, T cell receptor" + "co-receptor CD8 + more" +Marker Key "1) { CCR3- } CD8-, CCR7-, CD4+ ( ) [ alpha-beta T cell receptor" + "complex+, receptor-type tyrosine-protein phosphatase C isoform" + "CD45RA+, CD3+ ] 2) { CCR3- } CD8-, CCR7-, CD4+ ( ) [ alpha-beta T" + "cell receptor complex+, C-X-C chemokine receptor type 5+, inducible" + "T-cell costimulator+, programmed cell death protein 1+, CD3+ ] 3) {" + "CCR3- } CD8-, CCR7-, CD4+ ( ) [ interleukin-2 receptor subunit" + "alpha-, receptor-type tyrosine-protein phosphatase C isoform CD45RA-," + "alpha-beta T cell receptor complex+, receptor-type tyrosine-protein" + "phosphatase C isoform CD45RO+, interleukin-7 receptor subunit alpha+," + "CD3+, CD44 moleculehi, interleukin-2 receptor subunit betahi ] 4) {" + "CCR3-, CCR7- } CD8-, CD4+ ( ) [ L-selectin-, interleukin-7 receptor" + "subunit alpha-, alpha-beta T cell receptor complex+, CD69 molecule+," + "interleukin-2 receptor subunit alpha+, ADP-ribosyl cyclase 1+, MHC" + "class II histocompatibility antigen alpha chain HLA-DRA+, CD3+ ] 5) {" + "CCR3-, CCR7- } CD8-, CD4+ ( ) [ interleukin-2 receptor subunit" + "alpha-, alpha-beta T cell receptor complex+, receptor-type" + "tyrosine-protein phosphatase C isoform CD45RO+, interleukin-7" + "receptor subunit alpha+, CD3+, CD44 moleculehi, interleukin-2" + "receptor subunit betahi ] + more" +Score (Out of 1) "1) 0.167 2) 0.125 3) 0.091 4) -0.2 5) -0.222 + more" +Cell ID "1) CL_0001044 2) CL_0002038 3) CL_0000905 4) CL_0001043 5) CL_0000897" + "+ more" +Cell Label "1) effector CD4-positive, alpha-beta T cell 2) T follicular helper" + "cell 3) effector memory CD4-positive, alpha-beta T cell 4) activated" + "CD4-positive, alpha-beta T cell, human 5) CD4-positive, alpha-beta" + "memory T cell + more"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/test-data/flowcl_pop03.txt Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,43 @@ + [,1] +Short marker names "CD4+CCR3-CD8+CCR7lo" +Ontology marker names "CD4 molecule, C-C chemokine receptor type 3, T cell receptor" + "co-receptor CD8, C-C chemokine receptor type 7" +Experiment markers "CD4,CCR3,CD8,CCR7" +Ontology exper. names "CD4 molecule, C-C chemokine receptor type 3, T cell receptor" + "co-receptor CD8, C-C chemokine receptor type 7" +Successful Match? "No" +Marker ID "1) PR_000001004 2) PR_000001004 3) PR_000001004 4) PR_000001004 5)" + "PR_000001004, PR_000025402 + more" +Marker Label "1) CD4 molecule 2) CD4 molecule 3) CD4 molecule 4) CD4 molecule 5)" + "CD4 molecule, T cell receptor co-receptor CD8 + more" +Marker Key "1) { CD8+, CCR3-, CCR7lo } CD4+ ( ) [ CD19 molecule-, CD34 molecule-," + "CD34 molecule-, neural cell adhesion molecule 1-, membrane-spanning" + "4-domains subfamily A member 1-, lymphocyte antigen 75-, T-cell" + "surface glycoprotein CD8 alpha chain-, CD83 molecule+, integrin" + "alpha-M+, MHC class II protein complexhi, CD86 moleculehi, CD80" + "moleculehi, integrin alpha-Xhi ] 2) { CD8+, CCR3-, CCR7lo } CD4+ ( )" + "[ CD19 molecule-, CD34 molecule-, CD34 molecule-, neural cell" + "adhesion molecule 1-, membrane-spanning 4-domains subfamily A member" + "1-, lymphocyte antigen 75-, T-cell surface glycoprotein CD8 alpha" + "chain-, integrin alpha-M+, MHC class II protein complexlo, CD86" + "moleculelo, CD80 moleculelo, integrin alpha-Xhi ] 3) { CD8+, CCR3-," + "CCR7lo } CD4+ ( ) [ CD19 molecule-, CD34 molecule-, CD34 molecule-," + "neural cell adhesion molecule 1-, membrane-spanning 4-domains" + "subfamily A member 1-, integrin alpha-M-, T-cell surface glycoprotein" + "CD8 alpha chain-, receptor-type tyrosine-protein phosphatase C" + "isoform CD45R+, lymphocyte antigen 6G+, integrin alpha-Xlo ] 4) {" + "CD8+, CCR3-, CCR7lo } CD4+ ( ) [ CD19 molecule-, CD34 molecule-, CD34" + "molecule-, neural cell adhesion molecule 1-, membrane-spanning" + "4-domains subfamily A member 1-, integrin alpha-M-, receptor-type" + "tyrosine-protein phosphatase C isoform CD45R+, lymphocyte antigen" + "6G+, T-cell surface glycoprotein CD8 alpha chain+, integrin alpha-Xlo" + "] 5) { CCR3-, CCR7lo } CD4+, CD8+ ( ) [ alpha-beta T cell receptor" + "complexlo, CD69 molecule+ ] + more" +Score (Out of 1) "1) -0.357 2) -0.385 3) -0.455 4) -0.455 5) -0.5 + more" +Cell ID "1) CL_0001003 2) CL_0000997 3) CL_0002455 4) CL_0002456 5) CL_0002429" + "+ more" +Cell Label "1) mature CD8_alpha-negative CD11b-positive dendritic cell 2)" + "immature CD8_alpha-negative CD11b-positive dendritic cell 3)" + "CD8_alpha-negative plasmactyoid dendritic cell 4) CD8_alpha-positive" + "plasmactyoid dendritic cell 5) CD69-positive double-positive" + "thymocyte + more"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/test-data/input.flowscore Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,4 @@ +Population_ID FSC SSC CD4 CCR3 CD8 CCR7 Count Percentage +1 1 1 3 1 1 1 1000 5 +2 1 1 3 1 1 1 1000 5 +3 1 1 3 1 3 2 1000 5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profile_cl/test-data/out.html Mon Feb 27 13:03:19 2017 -0500 @@ -0,0 +1,91 @@ +<!DOCTYPE html> +<html> +<head lang="en"> +<title>FLOCK Populations Ontology</title> +<meta charset="UTF-8"> +<meta HTTP-EQUIV="Pragma" CONTENT="no-cache"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<link rel="stylesheet" href="/static/flowtools/bootstrap/css/bootstrap.css"/> +<link rel="stylesheet" href="/static/flowtools/select2/select2.min.css"/> +<link rel="stylesheet" href="/static/flowtools/css/flowCL.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/datatables.min.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/Buttons-1.1.2/css/buttons.dataTables.min.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/Select-1.1.2/css/select.dataTables.min.css"/> +<script src="/static/flowtools/jquery-1.11.3.min.js" type="text/javascript"></script> +<script src="/static/flowtools/bootstrap/js/bootstrap.js" type="text/javascript"></script> +<script src="/static/flowtools/select2/select2.full.min.js" type="text/javascript"></script> +<script src="/static/flowtools/d3/d3.min.js" type="text/javascript"></script> +<script src="/static/flowtools/datatables/datatables.min.js" type="text/javascript"></script> +<script src="/static/flowtools/js/profileCLs.js" type="text/javascript"></script> + +<style> +#input{font-family:Calibri,Arial} +table.dataTable tbody td.dt-body-right { + text-align: right; +} +#div{padding:5px;width:150px;height:100px;text-align:center} +table{width:100%;border:0px solid;border-collapse:collapse;text-align:center;} +th{background-color:#3e6db0;color:#fff;padding:5px;text-align:center} +</style> +</head> + +<body> +<div class="container-fluid"> + <div class="row" style="padding-bottom:10px;min-height:500px;"> + <div class="col-md-12" > + <ul class="nav nav-tabs tabs-main"> + <li class="homeTab active" data-value="clprofiles"><a href="#clprofiles" data-toggle="tab">Populations Cell Ontologies</a></li> + <li class="homeTab" data-value="scores"><a href="#scores" data-toggle="tab">Populations Score Profiles</a></li> + </ul> + + <div class="tab-content"> + <div class="tab-pane active" id="clprofiles" style="min-height:500px;"> + <div class="row"> + <div id="clprof"/> + </div> + </div> + </div> + <div class="tab-pane" id="scores" style="height:800px;"> + <div class="row"> + <div id="clprof"/> + </div> + </div> + </div> + </div> + </div> +</div> + + +</div> +</div> + + +<script> +var clprofilesLoaded = false; +var scoresLoaded = false; + +$().ready(function() { + $(document).on('shown.bs.tab','a[data-toggle="tab"]', function(e) { + var tab = e.target.getAttribute("href"); + if (tab == '#clprofiles') { + if (clprofilesLoaded) { + return true; + } + clprofilesLoaded = true; + displayCLTable(); + } + if (tab == '#scores') { + if (scoresLoaded) { + return true; + } + scoresLoaded = true; + displayScoresTable(); + } + }); + + clprofilesLoaded = true; + displayCLTable(); +}); +</script> +</body> +</html>