From e4aeb4a272a2b6f50ab06b3dbbe22a6e7d33cc26 Mon Sep 17 00:00:00 2001 From: mariabernard Date: Wed, 21 Jun 2017 12:26:42 +0200 Subject: [PATCH] add FROGS Phyloseq Manova --- RELEASES_NOTES.md | 2 + app/r_manova.Rmd | 1 + app/r_manova.py | 1 + app/r_manova.xml | 1 + img/phyloseq_manova.png | Bin 0 -> 34162 bytes tools/phylo_clustering/data/Bray_Curtis.tsv | 65 ---------- tools/phylo_manova/data/Unifrac.tsv | 65 ++++++++++ tools/phylo_manova/data/data.Rdata | Bin 0 -> 46560 bytes tools/phylo_manova/r_manova.Rmd | 136 ++++++++++++++++++++ tools/phylo_manova/r_manova.py | 101 +++++++++++++++ tools/phylo_manova/r_manova.xml | 93 +++++++++++++ tools/phylo_manova/test.sh | 17 +++ 12 files changed, 417 insertions(+), 65 deletions(-) create mode 120000 app/r_manova.Rmd create mode 120000 app/r_manova.py create mode 120000 app/r_manova.xml create mode 100755 img/phyloseq_manova.png delete mode 100755 tools/phylo_clustering/data/Bray_Curtis.tsv create mode 100755 tools/phylo_manova/data/Unifrac.tsv create mode 100755 tools/phylo_manova/data/data.Rdata create mode 100755 tools/phylo_manova/r_manova.Rmd create mode 100755 tools/phylo_manova/r_manova.py create mode 100755 tools/phylo_manova/r_manova.xml create mode 100755 tools/phylo_manova/test.sh diff --git a/RELEASES_NOTES.md b/RELEASES_NOTES.md index 0047ed67..bd4b1f49 100644 --- a/RELEASES_NOTES.md +++ b/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 diff --git a/app/r_manova.Rmd b/app/r_manova.Rmd new file mode 120000 index 00000000..fe7e3164 --- /dev/null +++ b/app/r_manova.Rmd @@ -0,0 +1 @@ +../tools/phylo_manova/r_manova.Rmd \ No newline at end of file diff --git a/app/r_manova.py b/app/r_manova.py new file mode 120000 index 00000000..f6379741 --- /dev/null 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index 02f17aa4..00000000 --- a/tools/phylo_clustering/data/Bray_Curtis.tsv +++ /dev/null @@ -1,65 +0,0 @@ - DLT0.LOT08 DLT0.LOT05 DLT0.LOT03 DLT0.LOT07 DLT0.LOT06 DLT0.LOT01 DLT0.LOT04 DLT0.LOT10 MVT0.LOT05 MVT0.LOT01 MVT0.LOT06 MVT0.LOT07 MVT0.LOT03 MVT0.LOT09 MVT0.LOT08 MVT0.LOT10 BHT0.LOT01 BHT0.LOT07 BHT0.LOT06 BHT0.LOT03 BHT0.LOT10 BHT0.LOT05 BHT0.LOT04 BHT0.LOT08 VHT0.LOT02 VHT0.LOT10 VHT0.LOT03 VHT0.LOT01 VHT0.LOT08 VHT0.LOT06 VHT0.LOT07 VHT0.LOT04 SFT0.LOT08 SFT0.LOT07 SFT0.LOT06 SFT0.LOT03 SFT0.LOT02 SFT0.LOT05 SFT0.LOT04 SFT0.LOT01 FST0.LOT07 FST0.LOT08 FST0.LOT05 FST0.LOT06 FST0.LOT01 FST0.LOT03 FST0.LOT10 FST0.LOT02 FCT0.LOT06 FCT0.LOT10 FCT0.LOT05 FCT0.LOT03 FCT0.LOT08 FCT0.LOT02 FCT0.LOT07 FCT0.LOT01 CDT0.LOT10 CDT0.LOT08 CDT0.LOT05 CDT0.LOT04 CDT0.LOT06 CDT0.LOT09 CDT0.LOT07 CDT0.LOT02 -DLT0.LOT08 0 0.239033964840416 0.724185014507595 0.380952380952381 0.362177846048814 0.739887352790579 0.268390510325994 0.617255504352278 0.94205495818399 0.947943335040109 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0.898532172725721 0.84715821812596 0.977470558115719 0.82326335552142 0.949479433350401 0.944017750469363 -DLT0.LOT03 0.724185014507595 0.817716333845366 0 0.724099675712579 0.708397337429596 0.737753882915173 0.808585082778631 0.679808841099164 0.912613073903397 0.905871309097116 0.877026796381635 0.776241679467486 0.873357228195938 0.874125277351084 0.91389315582864 0.966291175968595 0.877197473971667 0.834016043693463 0.849974398361495 0.831541218637993 0.850486431131592 0.84963304318143 0.840672469704728 0.839563065369517 0.885987369858338 0.908175456562553 0.820276497695853 0.859276327018263 0.862604540023895 0.878989588667008 0.892046424304489 0.883768561187916 0.949820788530466 0.838880355009387 0.877282812766684 0.85279057859703 0.865164703874381 0.992916880013654 0.952295613585936 0.921232292200034 0.769926608636286 0.890595664789213 0.888803550093873 0.881037719747397 0.921402969790067 0.84220856801502 0.831029185867896 0.868748933265062 0.887779484553678 0.844171360300393 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0.681515616999488 0.84647550776583 0.850913125106673 0.991807475678443 0.954173067076293 0.920464243044888 0.788871821129886 0.879586960232122 0.876770779996586 0.871223758320533 0.916538658474142 0.618023553507424 0.800307219662058 0.870797064345451 0.809267793138761 0.84468339307049 0.934715821812596 0.896142686465267 0.721198156682028 0.862775217613927 0.753968253968254 0.879330943847073 0.96594982078853 0.891363713944359 0.780593958013313 0.772401433691756 0.975678443420379 0.81199863457928 0.927035330261137 0.873613244580987 -DLT0.LOT01 0.739887352790579 0.748847926267281 0.737753882915173 0.647380098993002 0.635176651305684 0 0.715821812596006 0.428912783751493 0.871991807475678 0.842976617170166 0.714029697900666 0.709762758149855 0.80568356374808 0.810121181088923 0.862348523638846 0.930960914831883 0.822665983956307 0.790407919440178 0.82147124082608 0.729390681003584 0.757125789383854 0.821385902031063 0.799027137736815 0.738521932070319 0.798344427376685 0.813961426864653 0.718808670421574 0.750810718552654 0.768817204301075 0.782215395118621 0.798088410991637 0.77931387608807 0.95852534562212 0.796552312681345 0.790237241850145 0.822922000341355 0.835125448028674 0.991551459293395 0.943335040109234 0.914831882573818 0.565454855777436 0.804574159412869 0.800307219662058 0.789639870285032 0.859617682198327 0.663082437275986 0.722990271377368 0.753712237583205 0.763867554190135 0.863543266769073 0.937190646868066 0.888206178528759 0.757125789383854 0.852107868236901 0.690305512886158 0.864567332309268 0.966376514763612 0.905359276327018 0.810803891449053 0.789127837514934 0.971582181259601 0.829749103942652 0.921658986175115 0.910138248847926 -DLT0.LOT04 0.268390510325994 0.314388120839734 0.808585082778631 0.363201911589008 0.348352961256187 0.715821812596006 0 0.608636286055641 0.930363543266769 0.929851510496672 0.909199522102748 0.929936849291688 0.877965523126813 0.919269499914661 0.945639187574671 0.966888547533709 0.869602321215224 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z=EZ=z{D~J0HptyvK17hD5=J*AhDL>Oy+^9k$aUvavLwP3CrNpxiX&pCQ^>D`~eSXw-4iH%(PxEsdGa(Kf1?2ipS++E;*O}nwb^go1i_N zsKnR8u!*Z-Ni$iQJtFBJTPHdYYgM`rD;6|d;63L9#~-p|LDb0TToYvT8{edmM&~k* z`lFtHgL^IXDzlC-^ky$PpRQiXgyt>qF zHEddo3HF~Ln}3gX9%%a?#(en+0%+(%OzUa;CH5ZdiC z3EMsv{4Je@X5G>~VJwI@tln*tJkcKi6Zo+vZ82qbLY=qeascroZ=4TPgG|JeArKd-Fxk^JXoKxr1;Y$Ut{?)tjBUTdWfSNYjf-l?u F_ + + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` +

FROGS Phyloseq: Multivariate Analysis of Variance

+ + 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 +

Loading packages & data

+```{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) +``` +

With adonis

+```{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)')) +``` + +

Through capscale

+```{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)") +``` + + + + + diff --git a/tools/phylo_manova/r_manova.py b/tools/phylo_manova/r_manova.py new file mode 100755 index 00000000..e2d91f5a --- /dev/null +++ b/tools/phylo_manova/r_manova.py @@ -0,0 +1,101 @@ +#!/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 . +# +__author__ = 'Ta Thi Ngan & Maria Bernard INRA - SIGENAE' +__copyright__ = 'Copyright (C) 2017 INRA' +__license__ = 'GNU General Public License' +__version__ = '1.0.0' +__email__ = 'frogs@toulouse.inra.fr' +__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 ) diff --git a/tools/phylo_manova/r_manova.xml b/tools/phylo_manova/r_manova.xml new file mode 100755 index 00000000..f4bde996 --- /dev/null +++ b/tools/phylo_manova/r_manova.xml @@ -0,0 +1,93 @@ + + + + with Canonical Analysis of Principal Coordinates + r_manova.py + --data $data + --varExp $varExp + --method $method + --html $html + + + + + + + + + + + + + + + + + + + +.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ 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 <https://en.wikipedia.org/wiki/HTML>`_): The review of Manova test. + +.. image:: ${static_path}/images/tools/frogs/phyloseq_manova.png + :height: 316 + :width: 927 + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@toulouse.inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + + diff --git a/tools/phylo_manova/test.sh b/tools/phylo_manova/test.sh new file mode 100755 index 00000000..fa92fa6a --- /dev/null +++ b/tools/phylo_manova/test.sh @@ -0,0 +1,17 @@ +#!/bin/sh +export PATH=../../libexec:$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