add FROGS Phyloseq Manova

RELEASES_NOTES.md

@@ -6,6 +6,8 @@
   * FROGS Phyloseq Alpha Diversity with richness plot
   * FROGS Phyloseq Beta Diversity distance matrix
   * FROGS Phyloseq Structure
+  * FROGS Phyloseq Clustering
+  * FROGS Phyloseq Manova 
 
 ### Bugs fixes:
   * Preprocess : min overlap at least equal to 1

app/r_manova.Rmd

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+../tools/phylo_manova/r_manova.Rmd

app/r_manova.py

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+../tools/phylo_manova/r_manova.py

app/r_manova.xml

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+../tools/phylo_manova/r_manova.xml

tools/phylo_manova/r_manova.Rmd

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+---
+output: html_document
+params:
+   data:
+      value: x
+   varExp:
+      value: x
+   method:
+      value: x
+---
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<style type="text/css">
+code.r{ /* Code block */
+  font-size: 11px;
+}
+pre{ /* Code block */
+  font-size: 11px
+}
+.button {
+    background-color: #2a7ecc; /* Blue */
+    border : none;
+    color  : white;
+    padding: 5px 10px;
+    text-align: center;
+    text-decoration: none;
+    display  : inline-block;
+    font-size: 12px;
+    margin   : 4px 2px;
+    cursor   : pointer;
+    border-radius: 8px;
+}
+h4 { 
+    display   : block;
+    font-size : 1em;
+    margin-top: 1.33em;
+    margin-bottom: 1.33em;
+    margin-left : 0;
+    margin-right: 0;
+    font-weight : bold;
+    color : #2a7ecc;
+}
+</style>
+
+<script src="https://s3-us-west-2.amazonaws.com/s.cdpn.io/14082/FileSaver.js"></script>
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+<h3>FROGS Phyloseq: Multivariate Analysis of Variance</h3>
+
+ Phyloseq `r packageVersion("phyloseq")`
+
+```{r include=FALSE, echo=FALSE}
+library(phyloseq)
+library(vegan)
+load(params$data)
+
+##get dist object from distance matrix file
+setwd(dirname(params$method))
+A        <- read.table(file=basename(params$method), row.names=1)
+dist.a   <- as.dist(A)
+metadata <- as(sample_data(data), "data.frame") ## convert sample_data to data.frame
+```
+
+#{.tabset .tabset-fade .tabset-pills}
+##Multivariate ANOVA performed with adonis
+```{r, echo=FALSE, cach=FALSE, comment=NA}
+adonis <- paste('adonis(dist.a ~ ', params$varExp, ', data = metadata, perm = 9999)')
+eval(parse(text = adonis))
+```
+
+##Canonical Analysis of Principal Coordinates through capscale
+```{r, echo=FALSE, cach=FALSE, comment=NA, warning=FALSE}
+capcap <- paste('cap <- capscale(dist.a ~ ', params$varExp, ', data = metadata)')
+eval(parse(text = capcap))
+cap
+anova(cap, permutations = 999)
+```
+
+##R code
+<h4>Loading packages & data</h4>
+```{r, eval=FALSE}
+library(vegan)
+## if in new session
+# library(phyloseq)
+#
+## load phyloseq object
+# data <- path to Rdata file
+# load(data)
+# extract sample metadata in a dataframe
+metadata <- as(sample_data(data), "data.frame")
+
+## load beta distance matrix
+method <- # path to Beta diversity tsv file
+A <- read.table(file=method, row.names=1)
+beta_dist <- as.dist(A)
+```
+<h4>With adonis</h4>
+```{r, comment=NA, cache=FALSE, echo=FALSE}
+cat(paste(sep="","## change experiment variable (currently ", params$varExp, " )if you wish\n","## Multivariate ANOVA performed with adonis",'\nadonis(beta_dist ~ ', params$varExp, ', data = metadata, perm = 9999)'))
+```
+
+<h4>Through capscale</h4>
+```{r, comment=NA, cache=FALSE, echo=FALSE}
+cat(paste(sep="","## change experiment variable (currently ", params$varExp, " ) if you wish\n", "## Canonical Analysis of Principal Coordinates through capscale",'\ncap <- capscale(beta_dist ~ ', params$varExp, ', data = metadata)'), "\nanova(cap, permutations = 999)")
+```
+
+<div id="code-r-file" style="display:none;">
+library(vegan)
+&#10;#if in new session
+&#10;#library(phyloseq)
+&#10;#data <- path to Rdata file
+&#10;#load(data)
+&#10;varExp <- #Experiment variable
+&#10;method <- # path to Beta diversity tsv file
+&#10;
+&#10;A <- read.table(file=basename(method), row.names=1) 
+&#10;dist.a <- as.dist(A) 
+&#10;metadata <- as(sample_data(data), \"data.frame\")
+&#10;
+&#10;capcap <- paste(\'adonis(dist.a ~ \',varExp, \', data = metadata, perm = 9999)\')
+&#10;eval(parse(text = capcap))
+&#10;
+&#10;capcap <- paste(\'cap <- capscale(dist.a ~ \',varExp, \', data = metadata)\')
+&#10;eval(parse(text = capcap))
+&#10;anova(cap, permutations = 999)
+</div>
+
+<script>
+  function download(){
+    var text = document.getElementById("code-r-file").textContent;
+    var blob = new Blob([text],{type:"text/plain;charset=utf-8"});
+    saveAs(blob,"manova_code.R");
+   }
+</script>
+<input type="button" value="Download R code" class="button" onclick="download();"/>

tools/phylo_manova/r_manova.py

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+#!/usr/bin/env python2.7
+#
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+__author__ = 'Ta Thi Ngan & Maria Bernard INRA - SIGENAE'
+__copyright__ = 'Copyright (C) 2017 INRA'
+__license__ = 'GNU General Public License'
+__version__ = '1.0.0'
+__email__ = '[email protected]'
+__status__ = 'prod'
+
+import os
+import sys
+import argparse
+CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
+# PATH
+BIN_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "libexec"))
+os.environ['PATH'] = BIN_DIR + os.pathsep + os.environ['PATH']
+# PYTHONPATH
+LIB_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "lib"))
+sys.path.append(LIB_DIR)
+if os.getenv('PYTHONPATH') is None: os.environ['PYTHONPATH'] = LIB_DIR
+else: os.environ['PYTHONPATH'] = os.environ['PYTHONPATH'] + os.pathsep + LIB_DIR
+
+from frogsUtils import *
+##################################################################################################################################################
+#
+# COMMAND LINES
+#
+##################################################################################################################################################
+
+class Rscript(Cmd):
+    """
+    @summary: Launch Rmarkdown script to Multivariate Analysis of Variance (MANOVA) test with CAP (Canonical Analysis of Principal Coordinates) by adonis.
+    @see: http://rmarkdown.rstudio.com/
+          https://joey711.github.io/phyloseq/
+    @return: the html file containing manova test result.
+    """
+    def __init__(self, html, data, varExp, matrix):
+        """
+        @param html: [str] The path to store resulting html file.
+        @param data: [str] One phyloseq object in Rdata file, the result of FROGS Phyloseq Import Data.
+        @param varExp: [str] The experiment variable.
+        @param matrix: [str] Path of data file containing beta diversity distance matrix. These file is the result of FROGS Phyloseq Beta Diversity.
+        """ 
+        rmd = os.path.join(CURRENT_DIR, "r_manova.Rmd")
+        Cmd.__init__( self,
+                      'Rscript',
+                      'Run 1 code Rmarkdown',
+                       '-e "rmarkdown::render('+"'"+rmd+"',output_file='"+html+"', params=list(data='"+data+"', varExp='"+varExp+"',method='"+matrix+"'), intermediates_dir='"+os.path.dirname(html)+"')"+'" 2> /dev/null',
+                       "-e '(sessionInfo()[[1]][13])[[1]][1]; paste(\"Rmarkdown version: \",packageVersion(\"rmarkdown\")) ; library(phyloseq); paste(\"Phyloseq version: \",packageVersion(\"phyloseq\"))'")
+    def get_version(self):
+        """
+        @summary: Returns the program version number.
+        @return: [str] Version number if this is possible, otherwise this method return 'unknown'.
+        """
+        return Cmd.get_version(self, 'stdout')
+
+##################################################################################################################################################
+#
+# MAIN
+#
+##################################################################################################################################################
+
+if __name__ == "__main__":
+
+    # Manage parameters
+    parser = argparse.ArgumentParser( description='Multivariate Analysis of Variance (MANOVA) test with CAP (Canonical Analysis of Principal Coordinates) by adonis.' )
+    parser.add_argument('-v', '--varExp', type=str, required=True, default=None, help='The experiment variable you want to analyse.')
+
+    # Inputs
+    group_input = parser.add_argument_group( 'Inputs' )
+    group_input.add_argument('-d','--data', required=True, default=None, help="The path of RData file containing a phyloseq object-the result of FROGS Phyloseq Import Data" )
+    group_input.add_argument('-m','--distance-matrix', required=True, default=None, help="The path of data file containing beta diversity distance matrix. These file is the result of FROGS Phyloseq Beta Diversity." ) 
+
+    # output
+    group_output = parser.add_argument_group( 'Outputs' )
+    group_output.add_argument('-o','--html', default='manova.html', help="The path to store resulting html file. [Default: %(default)s]" )   
+    group_output.add_argument( '-l', '--log_file', default=sys.stdout, help='This output file will contain several information on executed commands.')    
+
+    args = parser.parse_args()
+    prevent_shell_injections(args)   
+    # Process 
+    Logger.static_write(args.log_file, "## Application\nSoftware :" + sys.argv[0] + " (version : " + str(__version__) + ")\nCommand : " + " ".join(sys.argv) + "\n\n")
+    html=os.path.abspath(args.html)
+    data=os.path.abspath(args.data)
+    matrix=os.path.abspath(args.distance_matrix)    
+    Rscript(html, data, args.varExp, matrix).submit( args.log_file )   

tools/phylo_manova/r_manova.xml

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+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2017 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool name="FROGS Phyloseq Multivariate Analysis Of Variance" id="FROGS_Phyloseq_Multivariate_Analysis_Of_Variance" version="1.0.0">
+	<description>with Canonical Analysis of Principal Coordinates</description>
+	<command interpreter="python">r_manova.py 
+                                    --data $data
+                                    --varExp $varExp
+                                    --method $method
+                                    --html $html
+	</command>
+    <inputs>
+		<!-- Files -->
+	    <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="These file is the result of FROGS Phyloseq Beta Diversity." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+		<!-- Parameters -->	
+		<param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>	
+    </inputs>
+	<outputs>
+		<data format="html" name="html" label="${tool.name}: manova.html" from_work_dir="manova.html"/>
+	</outputs>
+	<help>
+
+.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png 
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and customized R function for testing Multivariate Analysis of Variance (MANOVA) with CAP (Canonical Analysis of Principal Coordinates) by adonis.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**data file** (format RData):
+The informations of data in one phyloseq object.
+This is the result of FROGS Phyloseq Import Data.
+
+**distance file** (format tabular):
+The data file containing beta diversity distance matrix.
+These file is the result of FROGS Phyloseq Beta Diversity. 
+
+.. class:: h3
+
+Output
+
+**html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The review of Manova test.
+
+.. image:: ${static_path}/images/tools/frogs/phyloseq_manova.png 
+     :height: 316
+     :width: 927
+
+.. class:: infomark page-header h2
+
+**Contact**
+
+Contacts: [email protected]
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+
+	</help>
+</tool>

tools/phylo_manova/test.sh

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+#!/bin/sh
+export PATH=../../libexec:$PATH
+export PYTHONPATH=../../lib:$PYTHONPATH
+
+if [ -d test ]
+then
+  rm -r test/*
+else
+  mkdir test
+fi 
+
+
+python r_manova.py --data data/data.Rdata \
+                   --varExp EnvType \
+                   --distance-matrix data/Unifrac.tsv \
+                   --html test/phylo_manova.html \
+                   -l test/phylo_manova.log