Mercurial > repos > iuc > dimet_timecourse_analysis
changeset 2:40edef7d7f74 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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--- a/dimet_timecourse_analysis.xml Tue Jan 23 14:56:42 2024 +0000 +++ b/dimet_timecourse_analysis.xml Thu Feb 15 12:50:27 2024 +0000 @@ -39,7 +39,7 @@ '++analysis.method.impute_values=${impute_values}' '++analysis.dataset.subfolder=' '++analysis.dataset.label=' - '++analysis.dataset.conditions=${conds}' + '++analysis.dataset.conditions=${conditions}' #if $metadata_path: '++analysis.dataset.metadata=metadata' #end if @@ -64,7 +64,7 @@ ]]></command> <inputs> <expand macro="input_parameters_diff_analysis"/> - <expand macro="conditions"/> + <expand macro="factor_list"/> <expand macro="correction_method"/> <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/> </inputs> @@ -80,8 +80,14 @@ <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/> <param name="correction_method" value="bonferroni"/> <param name="qualityDistanceOverSpan" value="-0.3"/> + <param name="statistical_test_type" value="parametric"/> <param name="stat_test" value="Tt"/> - <param name="conditions" value='Control,L-Cycloserine'/> + <repeat name="plot_factor_list"> + <param name="condition" value="Control"/> + </repeat> + <repeat name="plot_factor_list"> + <param name="condition" value="L-Cycloserine"/> + </repeat> <output_collection name="report" type="list" count="4"> <element file="abundance--cell-Control-T2h-Control-T0-Tt.tsv" name="abundance--cell-Control-T2h-Control-T0-Tt.tsv" ftype="tabular"/> <element file="abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" name="abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/> @@ -259,11 +265,15 @@ The output consists of tables with the computed metrics, one by each pair of timepoints compared. The number of output tables = number-of-conditions x (number-of-timepoints)-1 x number-of-compartments. +For more information about the implemented statistical tests, please visit: https://github.com/cbib/DIMet/wiki/2-Statistical-tests + +The output files are explained in https://github.com/cbib/DIMet/wiki/3-Output + **Available data for testing** -You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent +You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent files for you are located in the subfolders inside the data folder). -You can also use the minimal data examples from https://zenodo.org/record/8380706 +You can also use the minimal data examples from https://zenodo.org/record/10579891 ]]> </help>
--- a/macros.xml Tue Jan 23 14:56:42 2024 +0000 +++ b/macros.xml Thu Feb 15 12:50:27 2024 +0000 @@ -1,42 +1,46 @@ <macros> - <token name="@TOOL_VERSION@">0.1.4</token> + <token name="@TOOL_VERSION@">0.2.1</token> <token name="@VERSION_SUFFIX@">1</token> <token name="@EXECUTABLE@">pca</token> - <xml name="factor_repeat"> - <repeat name="rep_factorName" title="Factor" min="1"> - <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers" - help="Only letters, numbers and underscores will be retained in this field"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> - </param> - <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> - <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" - help="Only letters, numbers and underscores will be retained in this field"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> - </param> - <yield/> - </repeat> - </repeat> - </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> </requirements> </xml> + <xml name="statistical_test_for_multigroup"> + <param name="stat_test" type="select" value="KW" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> + <option value="KW">Kruskal-Wallis</option> + </param> + </xml> <xml name="statistical_test"> - <param name="stat_test" type="select" value="Tt" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> - <option value="Tt">t-test</option> - <option value="MW">Mann Whitney</option> - <option value="KW">Kruskall Wallis</option> - <option value="ranksum">Wilcoxon's rank sum test</option> - <option value="Wcox">Wilcoxon signed-rank test</option> - <option value="BrMu">Brunner-Munzel test</option> - <option value="prm-scipy">permutations test</option> - <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option> - </param> + <conditional name="statistics"> + <param name="statistical_test_type" type="select" label="Choose which type of statistical test to perform" help="Choose which type of statistical test to perform"> + <option value="parametric">parametric</option> + <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option> + <option value="non-parametric-distribution">non-parametric (distribution based)</option> + </param> + <when value="parametric"> + <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> + <option value="Tt" selected="true">t-test</option> + </param> + </when> + <when value="non-parametric-rank"> + <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> + <option value="MW">Mann Whitney</option> + <option value="KW">Kruskal-Wallis</option> + <option value="ranksum" selected="true">Wilcoxon's rank sum test</option> + <option value="Wcox">Wilcoxon signed-rank test</option> + <option value="BrMu">Brunner-Munzel test</option> + </param> + </when> + <when value="non-parametric-distribution"> + <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> + <option value="prm-scipy" selected="true">permutations test</option> + <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option> + </param> + </when> + </conditional> + </xml> <xml name="citations"> <citations> @@ -86,14 +90,14 @@ </xml> <xml name="input_parameters_metabologram"> <conditional name="data_input"> - <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance, mean enrichment or isotopologue files"> + <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance and mean enrichment files"> <option value="abundance" selected="True">abundance</option> <option value="mean_enrichment">mean_enrichment</option> </param> <when value="abundance"> <expand macro="abundance_file_macros"/> <param name="metabolites_list" type="select" optional="false" multiple="true" - label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> + label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> <validator type="length" min="1" message="Please enter at max 2 compartments"/> <options from_dataset="abundance_file"> <column name="metabolite_or_isotopologue" index="0"/> @@ -115,7 +119,7 @@ <when value="mean_enrichment"> <expand macro="enrichment_file_macros"/> <param name="metabolites_list" type="select" optional="false" multiple="true" - label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> + label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> <validator type="length" min="1" message="Please enter at max 2 compartments"/> <options from_dataset="me_or_frac_contrib_file"> <column name="metabolite_or_isotopologue" index="0"/> @@ -139,9 +143,33 @@ <param name="path_kegg_transcripts" type="data" format="tabular" label="Pathways kegg transcripts file" help="A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/> <expand macro="metadata_file_macros"/> </xml> + <xml name="input_parameters_bivar_analysis"> + <conditional name="data_input"> + <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files"> + <option value="abundance" selected="True">abundance</option> + <option value="mean_enrichment">mean_enrichment</option> + <option value="isotop_prop">isotop_prop</option> + <option value="isotop_abs">isotop_abs</option> + </param> + <when value="abundance"> + <expand macro="abundance_file_macros"/> + + </when> + <when value="mean_enrichment"> + <expand macro="enrichment_file_macros"/> + </when> + <when value="isotop_prop"> + <expand macro="isotopologue_prop_file_macros"/> + </when> + <when value="isotop_abs"> + <expand macro="isotopologue_abs_file_macros"/> + </when> + </conditional> + <expand macro="metadata_file_macros"/> + </xml> <xml name="input_parameters_diff_analysis"> <conditional name="data_input"> - <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance and mean enrichment files"> + <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files"> <option value="abundance" selected="True">abundance</option> <option value="mean_enrichment">mean_enrichment</option> <option value="isotop_prop">isotop_prop</option> @@ -167,6 +195,34 @@ </conditional> <expand macro="metadata_file_macros"/> </xml> + <xml name="input_parameters_multi_diff_analysis"> + <conditional name="data_input"> + <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files"> + <option value="abundance" selected="True">abundance</option> + <option value="mean_enrichment">mean_enrichment</option> + <option value="isotop_prop">isotop_prop</option> + <option value="isotop_abs">isotop_abs</option> + </param> + <when value="abundance"> + <expand macro="abundance_file_macros"/> + <expand macro="statistical_test_for_multigroup"/> + + </when> + <when value="mean_enrichment"> + <expand macro="enrichment_file_macros"/> + <expand macro="statistical_test_for_multigroup"/> + </when> + <when value="isotop_prop"> + <expand macro="isotopologue_prop_file_macros"/> + <expand macro="statistical_test_for_multigroup"/> + </when> + <when value="isotop_abs"> + <expand macro="isotopologue_abs_file_macros"/> + <expand macro="statistical_test_for_multigroup"/> + </when> + </conditional> + <expand macro="metadata_file_macros"/> + </xml> <xml name="suffix"> <param name="suffix" type="text" optional="false" label="suffix to add to output files" > <sanitizer invalid_char=""> @@ -177,7 +233,7 @@ </param> </xml> <xml name="conditions"> - <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to metabolite list"> + <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to condition list"> <options from_dataset="metadata_path"> <column name="condition" index="1"/> <column name="value" index="1"/> @@ -232,7 +288,7 @@ </param> </xml> <xml name="timepoint"> - <param name="timepoint" type="select" optional="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if two conditions are set.)"> + <param name="timepoint" type="select" optional="false" multiple="true" label="Browse timepoint from metadata file (1 min.)"> <options from_dataset="metadata_path"> <column name="timepoint" index="2"/> <column name="value" index="2"/> @@ -307,6 +363,25 @@ </sanitizer> </param> </xml> + <xml name="compartments_metabologram"> + <param name="compartments" type="select" optional="false" multiple="false" + label="Browse compartments from metadata file (1 max.). You have to load a metadata file prior to have access to compartments"> + <options from_dataset="metadata_path"> + <column name="compartment" index="4"/> + <column name="value" index="4"/> + <filter type="unique_value" name="compartment" column="4"/> + <filter type="remove_value" value="compartment"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </xml> <xml name="compartments"> <param name="compartments" type="select" optional="false" multiple="true" label="Browse compartments from metadata file (1 min.). You have to load a metadata file prior to have access to compartments"> @@ -328,7 +403,7 @@ </xml> <xml name="abundance_metabolites_list"> <param name="metabolites_list" type="select" optional="false" multiple="true" - label="Select Metabolite(s) for factor 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list"> + label="Select Metabolite(s) for condition 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list"> <validator type="length" min="1" message="Please enter at max 2 compartments"/> <options from_dataset="abundance_file"> <column name="metabolite_or_isotopologue" index="0"/> @@ -348,8 +423,8 @@ </xml> <xml name="enrichment_metabolites_list"> <param name="metabolites_list" type="select" optional="false" multiple="true" - label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> - <validator type="length" min="1" message="Please enter at max 2 compartments"/> + label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> + <validator type="length" min="1" message="Please enter at min 1 metabolite"/> <options from_dataset="me_or_frac_contrib_file"> <column name="ID" index="0"/> <column name="value" index="0"/> @@ -369,7 +444,7 @@ <xml name="isotopologue_metabolites_list"> <param name="metabolites_list" type="select" optional="false" multiple="true" label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> - <validator type="length" min="1" message="Please enter at max 2 compartments"/> + <validator type="length" min="1" message="Please enter at min 1 metabolite"/> <options from_dataset="isotop_prop_file"> <column name="ID" index="0"/> <column name="value" index="0"/> @@ -387,27 +462,132 @@ </param> </xml> <xml name="deg_list"> - <repeat name="deg_list" title="Deregulated gene set"> + <repeat name="deg_list" title="Deregulated gene set" default="1" min="1"> <param name="input" type="data" format="tabular" label="Deregulated genes set"/> <param name="idcol" type="data_column" data_ref="input" label="Column for id" use_header_names="true"/> <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/> + <param name="timepoint" type="select" optional="false" multiple="false" label="Browse timepoint from metadata file (1 min.)"> + <options from_dataset="metadata_path"> + <column name="timepoint" index="2"/> + <column name="value" index="2"/> + <filter type="unique_value" name="timepoint" column="2"/> + <filter type="remove_value" value="timepoint"/> + <filter type="sort_by" name="timepoint" column="1"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list"> + <param name="condition" label="Condition" type="select" optional="false" multiple="false"> + <options from_dataset="metadata_path"> + <column name="condition" index="1"/> + <column name="value" index="1"/> + <filter type="unique_value" name="condition" column="condition"/> + <filter type="remove_value" value="condition"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </repeat> + </repeat> </xml> + <xml name="plot_abundance_factor_list"> + <repeat name="plot_abundance_factor_list" title="Conditions" min="1" help="Specify conditions to compare from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to condition list"> + <param name="condition" label="Condition" type="select" optional="false" multiple="false"> + <options from_dataset="metadata_path"> + <column name="condition" index="1"/> + <column name="value" index="1"/> + <filter type="unique_value" name="condition" column="condition"/> + <filter type="remove_value" value="condition"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </repeat> + </xml> + <xml name="plot_factor_list"> + <repeat name="plot_factor_list" title="Conditions" min="2" help="Specify conditions to compare from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to condition list"> + <param name="condition" label="Condition" type="select" optional="false" multiple="false"> + <options from_dataset="metadata_path"> + <column name="condition" index="1"/> + <column name="value" index="1"/> + <filter type="unique_value" name="condition" column="condition"/> + <filter type="remove_value" value="condition"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </repeat> + </xml> + <xml name="factor_list"> + <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list"> + <param name="condition" label="Condition" type="select" optional="false" multiple="false"> + <options from_dataset="metadata_path"> + <column name="condition" index="1"/> + <column name="value" index="1"/> + <filter type="unique_value" name="condition" column="condition"/> + <filter type="remove_value" value="condition"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </repeat> + </xml> + <xml name="palette"> + <param name="palette" type="select" value="pastel" display="radio" label="Select palette colormap to apply to abundance plot." help="For more information see https://seaborn.pydata.org/tutorial/color_palettes.html"> + <option value="pastel" selected="true">pastel</option> + <option value="deep">deep</option> + <option value="muted">muted</option> + <option value="bright">bright</option> + <option value="dark">dark</option> + <option value="colorblind">colorblind</option> + </param> + </xml> <token name="@INIT_PCA@"><![CDATA[ #import json #import re - mkdir -p data/raw && - mkdir -p data/processed && + mkdir -p data && #if $metadata_path: - ln -s '$metadata_path' data/raw/metadata.csv && + ln -s '$metadata_path' data/metadata.csv && #end if #if $abundance_file: - ln -s '$abundance_file' data/raw/abundance.csv && + ln -s '$abundance_file' data/abundance.csv && #end if #if $me_or_frac_contrib_file: - ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && + ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && #end if ]]></token> @@ -420,68 +600,102 @@ ]]></token> <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[ - mkdir -p data/raw && - mkdir -p data/processed && + mkdir -p data && #if $metadata_path: - ln -s '$metadata_path' data/raw/metadata.csv && + ln -s '$metadata_path' data/metadata.csv && #end if #if $abundance_file: - ln -s '$abundance_file' data/raw/abundance.csv && + ln -s '$abundance_file' data/abundance.csv && #end if ]]></token> <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[ - mkdir -p data/raw && - mkdir -p data/processed && + mkdir -p data && #if $metadata_path: - ln -s '$metadata_path' data/raw/metadata.csv && + ln -s '$metadata_path' data/metadata.csv && #end if #if $me_or_frac_contrib_file: - ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && + ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && #end if ]]></token> <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[ - mkdir -p data/raw && - mkdir -p data/processed && + mkdir -p data && + + #if $metadata_path: + ln -s '$metadata_path' data/metadata.csv && + #end if + #if $isotop_prop_file: + ln -s '$isotop_prop_file' data/isotop_prop.csv && + #end if + ]]></token> + <token name="@INIT_BI_ANALYSIS@"><![CDATA[ + + mkdir -p data && #if $metadata_path: - ln -s '$metadata_path' data/raw/metadata.csv && + ln -s '$metadata_path' data/metadata.csv && #end if - #if $isotop_prop_file: - ln -s '$isotop_prop_file' data/raw/isotop_prop.csv && + #set conditions_MDV_comparison = {} + #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson' + #set timepoints_MDV_comparison = {} + #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson' + #set conditions_metabolite_time_profiles = {} + #silent $conditions_metabolite_time_profiles['abundances']='pearson' + #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson' + + #set $impute_values = {} + #if str( $data_input.data_input_selector ) == "abundance": + #if $data_input.abundance_file: + ln -s '$data_input.abundance_file' data/abundance.csv && + #silent $impute_values['abundances']='min' + #end if + #elif str( $data_input.data_input_selector ) == "mean_enrichment": + #if $data_input.me_or_frac_contrib_file: + ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && + #silent $impute_values['mean_enrichment']='min' + #end if + #elif str( $data_input.data_input_selector ) == "isotop_prop": + #if $data_input.isotop_prop_file: + ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && + #silent $impute_values['isotopologue_proportions']='min' + #end if + #else + #if $data_input.isotop_abs_file: + ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && + #silent $impute_values['isotopologues']='min' + #end if #end if ]]></token> <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[ - mkdir -p data/raw && - mkdir -p data/processed && + mkdir -p data && #if $metadata_path: - ln -s '$metadata_path' data/raw/metadata.csv && + ln -s '$metadata_path' data/metadata.csv && #end if #set $impute_values = {} #if str( $data_input.data_input_selector ) == "abundance": #if $data_input.abundance_file: - ln -s '$data_input.abundance_file' data/raw/abundance.csv && + ln -s '$data_input.abundance_file' data/abundance.csv && #silent $impute_values['abundances']='min' #end if #elif str( $data_input.data_input_selector ) == "mean_enrichment": #if $data_input.me_or_frac_contrib_file: - ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && + ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && #silent $impute_values['mean_enrichment']='min' #end if #elif str( $data_input.data_input_selector ) == "isotop_prop": #if $data_input.isotop_prop_file: - ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv && + ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && #silent $impute_values['isotopologue_proportions']='min' #end if #else #if $data_input.isotop_abs_file: - ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv && + ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && #silent $impute_values['isotopologues']='min' #end if #end if @@ -493,69 +707,66 @@ #import csv #import subprocess - mkdir -p data/raw && - mkdir -p data/processed && - mkdir -p data/integration_files && + mkdir -p data && #if $path_kegg_metabolites: - ln -s '$path_kegg_metabolites' data/integration_files/pathways_kegg_metabolites.csv && + ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv && #end if #if $path_kegg_transcripts: - ln -s '$path_kegg_transcripts' data/integration_files/pathways_kegg_transcripts.csv && + ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv && #end if #if $metadata_path: - ln -s '$metadata_path' data/raw/metadata.csv && + ln -s '$metadata_path' data/metadata.csv && #end if #set $impute_values = {} #if str( $data_input.data_input_selector ) == "abundance": #if $data_input.abundance_file: - ln -s '$data_input.abundance_file' data/raw/abundance.csv && + ln -s '$data_input.abundance_file' data/abundance.csv && #silent $impute_values['abundances']='min' #end if #else: #if $data_input.me_or_frac_contrib_file: - ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && + ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && #silent $impute_values['mean_enrichment']='min' #end if #end if #for $i, $s in enumerate($deg_list) #set $cpt = str($i+1) - ln -s '${s.input}' data/integration_files/DEG_comparison'${cpt}'.csv && + ln -s '${s.input}' data/DEG_comparison'${cpt}'.csv && #end for ]]></token> <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[ - mkdir -p data/raw && - mkdir -p data/processed && + mkdir -p data && #if $metadata_path: - ln -s '$metadata_path' data/raw/metadata.csv && + ln -s '$metadata_path' data/metadata.csv && #end if #set $impute_values = {} #if str( $data_input.data_input_selector ) == "abundance": #if $data_input.abundance_file: - ln -s '$data_input.abundance_file' data/raw/abundance.csv && + ln -s '$data_input.abundance_file' data/abundance.csv && #silent $impute_values['abundances']='min' #end if #elif str( $data_input.data_input_selector ) == "mean_enrichment": #if $data_input.me_or_frac_contrib_file: - ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && + ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && #silent $impute_values['mean_enrichment']='min' #end if #elif str( $data_input.data_input_selector ) == "isotop_prop": #if $data_input.isotop_prop_file: - ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv && + ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && #silent $impute_values['isotopologue_proportions']='min' #end if #else #if $data_input.isotop_abs_file: - ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv && + ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && #silent $impute_values['isotopologues']='min' #end if #end if @@ -619,6 +830,20 @@ $conds.append(re.sub('"', '', str($co))) #end for ]]></token> + <token name="@INIT_PLOT_CONDITIONS@"><![CDATA[ + #set $conditions = list() + #for $i, $s in enumerate($plot_factor_list) + #set $cpt = str($i+1) + $conditions.append(re.sub('"', '', str($s.condition))) + #end for + ]]></token> + <token name="@INIT_ABUNDANCE_PLOT_CONDITIONS@"><![CDATA[ + #set $conditions = list() + #for $i, $s in enumerate($plot_abundance_factor_list) + #set $cpt = str($i+1) + $conditions.append(re.sub('"', '', str($s.condition))) + #end for + ]]></token> <token name="@INIT_TIMEPOINTS@"><![CDATA[ #import re @@ -641,7 +866,10 @@ #for $cp in $compartments: #silent $metabolites[re.sub('"', '', str($cp))]=list() #for $met in $metabolites_list: - $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str($met))) + #set tmp_met=re.sub('\,', '%%',str($met)) + #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0]) + #set tmp_met_ter=re.sub('%%', '\,',str($tmp_met_bis)) + $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter))) #end for #end for ]]></token> @@ -681,10 +909,43 @@ ]]></token> <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[ #import re - #set $conds = list() - #for $co in $conditions: - $conds.append(re.sub('"', '', str($co))) + #set $conditions = list() + #for $i, $s in enumerate($factor_list) + #set $cpt = str($i+1) + $conditions.append(re.sub('"', '', str($s.condition))) + #end for + + ]]></token> + <token name="@INIT_BIVAR_COMPARISONS@"><![CDATA[ + #import re + #set $conditions = list() + #for $i, $s in enumerate($plot_factor_list) + #set $cpt = str($i+1) + $conditions.append(re.sub('"', '', str($s.condition))) #end for + ]]></token> + <token name="@INIT_COMPARISONS_METABOLOGRAM@"><![CDATA[ + #import re + #set $conditions = list() + #set $timepoints = list() + #set $comparisons = list() + #for $i, $s in enumerate($deg_list) + #set $cpt = str($i+1) + #set $comparisons_bis = list() + #for $j, $t in enumerate($s.factor_list) + #set $sub_comparisons = list() + #if str($t.condition) not in $conditions: + $conditions.append(re.sub('"', '', str($t.condition))) + #end if + $sub_comparisons.append(re.sub('"', '', str($t.condition))) + $sub_comparisons.append(re.sub('"', '', str($s.timepoint))) + $comparisons_bis.append($sub_comparisons) + #end for + $timepoints.append(re.sub('"', '', str($s.timepoint))) + $comparisons.append($comparisons_bis) + #end for + + ]]></token> <token name="@INIT_COMPARISONS@"><![CDATA[ @@ -753,6 +1014,75 @@ #end if #end if ]]></token> + <token name="@INIT_DIFF_ANALYSIS_COMPARISONS@"><![CDATA[ + #import re + #set $conditions = list() + #for $i, $s in enumerate($factor_list) + #set $cpt = str($i+1) + $conditions.append(re.sub('"', '', str($s.condition))) + #end for + + #set $timepoints = list() + #for $tp in $timepoint: + $timepoints.append(re.sub('"', '', str($tp))) + #end for + + #set $comparisons = list() + #if len($conditions) > 1: + #if len($timepoints) > 0: + #for $tp in $timepoint: + #set $ctrl_found=False + #set $ctrl="" + #set $comparisons_bis = list() + + #for $co in $conditions: + #set $sub_comparisons = list() + #if str($co) in ["'Control'", "'control'", "'ctrl'"]: + #set $ctrl_found=True + #set $ctrl=str($co) + #else: + $sub_comparisons.append(re.sub('"', '', str($co))) + $sub_comparisons.append(re.sub('"', '', str($tp))) + + #end if + $comparisons_bis.append($sub_comparisons) + #end for + + #if $ctrl_found: + $sub_comparisons.append(str($ctrl)) + $sub_comparisons.append(str($tp)) + $comparisons_bis.append($sub_comparisons) + #end if + + $comparisons.append($comparisons_bis) + #end for + #else + #for $co in $conditions: + $comparisons.append(re.sub('"', '', str($co))) + #end for + #end if + + #else + #if len($conditions) > 0: + #if len($timepoints) > 1: + #for $co in $conditions: + #set $comparisons_bis = list() + #for $tp in $timepoint: + #set $sub_comparisons = list() + $sub_comparisons.append(re.sub('"', '', str($co))) + $sub_comparisons.append(re.sub('"', '', str($tp))) + $comparisons_bis.append($sub_comparisons) + #end for + $comparisons.append($comparisons_bis) + #end for + #end if + #else + #for $tp in $timepoint: + $comparisons.append(re.sub('"', '', str($tp))) + #end for + #end if + #end if + ]]></token> <token name="@INIT_TRANSCRIPTS@"><![CDATA[ #import re #import os
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CorrectedIsotopologues_5.csv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,52 @@ +ID MCF001089_TD01 MCF001089_TD02 MCF001089_TD07 MCF001089_TD08 MCF001089_TD19 MCF001089_TD20 MCF001089_TD25 MCF001089_TD26 MCF001089_TD37 MCF001089_TD38 MCF001089_TD43 MCF001089_TD44 MCF001089_TD55 MCF001089_TD56 MCF001089_TD61 MCF001089_TD62 +Fructose_1,6-bisphosphate_m+0 1 0 1 0.5 0.9 +Fructose_1,6-bisphosphate_m+1 0 0 0 0 0.001 0 +Fructose_1,6-bisphosphate_m+2 0 0 0 0 0 +Fructose_1,6-bisphosphate_m+3 0 0 0 0 0 +Fructose_1,6-bisphosphate_m+4 0 1 0 0.5 0.001 0.1 +Fructose_1,6-bisphosphate_m+5 0 0 0 0 0 +Fructose_1,6-bisphosphate_m+6 0 0 0 0 0 +Fumaric_acid_m+0 1 1 0.9979 1 1 +Fumaric_acid_m+1 0 0 0 0 0 +Fumaric_acid_m+2 0 0 0.0043 0 0.0009 +Fumaric_acid_m+3 0.0004 0.0006 0 0 0.0013 +Fumaric_acid_m+4 0.0003 0.0004 0.0004 0.0003 0.0005 0.0003 +Glycine_m+0 0.5 0.5 0.25 0.3 0.001 0.001 0.2 0 0.7 0.6 0.25 0.3 +Glycine_m+1 0.2 0.2 0.55 0.6 0.2 0.2 0.3 0.5 0.3 0.4 0.55 0.6 +Glycine_m+2 0.001 0.001 0 0.1 0.5 0.5 0.5 0.5 0 0 0 0.1 +L-Alanine_m+0 0.7 0.77 1 1 0 0 0.7 0.77 +L-Alanine_m+1 0.3 0.23 0 0 0.01 0.01 0.3 0.23 +L-Alanine_m+2 0.01 0.01 0 0.0002 0.211 0.211 0 0 +L-Alanine_m+3 0 0 0.0055 0.0069 0.699 0.699 0 0 0 0 0 0.0037 0 0 0 0 +L-Arginine_m+0 0.07 0.07 0 0 0.0001 0.0001 0 0 1 0 0 0 0 0 0 0 +L-Arginine_m+1 0.06 0.06 0 0 0.02 0.02 0 1 0 0 0 0 0 0 0 1 +L-Arginine_m+2 0.05 0.05 0 0 0.03 0.03 0 0 0 0 0 0 1 0 0 0 +L-Arginine_m+3 0.04 0.04 1 1 0.04 0.04 1 0 0 1 1 1 0 1 1 0 +L-Arginine_m+4 0.03 0.03 0 0 0.05 0.05 0 0 0 0 0 0 0 0 0 0 +L-Arginine_m+5 0.02 0.02 0 0 0.06 0.06 0 0 0 0 0 0 0 0 0 0 +L-Arginine_m+6 0.0001 0.0001 0 0 0.07 0.07 0 0 0 0 0 0 0 0 0 0 +L-Aspartic_acid_m+0 0.9863 0.9866 0.745 0.7303 0 0.001 0.7523 0.7437 +L-Aspartic_acid_m+1 0.0004 0 0.0716 0.0701 0.0014 0.0021 0.0635 0.063 +L-Aspartic_acid_m+2 0.0117 0.0131 0.1214 0.1303 0.0159 0.0141 0.1137 0.1193 +L-Aspartic_acid_m+3 0.0016 0.0008 0.055 0.0573 0.2 0.18 0.0589 0.0596 +L-Aspartic_acid_m+4 0 0 0.007 0.012 0 0 0.0117 0.0143 +L-Glutamic_acid_m+0 0.5 0.5 0.5577 0.5714 0.001 0.001 0.5577 0.5556 +L-Glutamic_acid_m+1 0.23 0.23 0.0737 0.0687 0.04 0.04 0.0715 0.0688 +L-Glutamic_acid_m+2 0.13 0.13 0.2485 0.2455 0.1 0.1 0.2477 0.2507 +L-Glutamic_acid_m+3 0.1 0.1 0.0619 0.057 0.13 0.13 0.0628 0.0625 +L-Glutamic_acid_m+4 0.04 0.04 0.0487 0.0477 0.23 0.23 0.0508 0.0506 +L-Glutamic_acid_m+5 0.001 0.001 0.0094 0.0096 0.5 0.5 0.0095 0.0118 +L-Glutamine_m+0 1 0.4 0.4 0.2 0.6673 +L-Glutamine_m+1 0 0.0347 0.34 0 0.0526 +L-Glutamine_m+2 0.01 0.1482 0.009 0.0104 0.1919 +L-Glutamine_m+3 0 0.2371 0 0 0.043 +L-Glutamine_m+4 0 0.0263 0 0.36 0.0374 +L-Glutamine_m+5 0 0.0053 0 0.04 0.0078 +L-Lactic_acid_m+0 0 0 0.9878 0.9883 0.9878 0.9883 0 0 0.0155 0.0168 0.0173 0.0191 0.0147 0.0135 0.0229 0.0165 +L-Lactic_acid_m+1 0 0 0.0122 0.0117 0.0122 0.0117 0 0 0.0002 0.0002 0.0002 0.0002 0.0002 0.0002 0.0001 0.0002 +L-Lactic_acid_m+2 0.0115 0.0121 0.0001 0 0.0001 0 0.0115 0.0121 0.0121 0.012 0.0121 0.012 0.012 0.0121 0.0118 0.0119 +L-Lactic_acid_m+3 0.9885 0.9879 0 0.0001 0 0.0001 0.9885 0.9879 0.9723 0.9709 0.9704 0.9687 0.9731 0.9742 0.9651 0.9713 +Pyruvic_acid_m+0 0.08 0.07 0.3 0.2 0.57 0.6 0.01 0.3 0.1 0.1 0.3 0.2 0.57 0.6 0.01 0.3 +Pyruvic_acid_m+1 0.12 0.13 0.3 0.6 0.23 0.2 0.15 0.2 0.1 0.1 0.3 0.6 0.23 0.2 0.15 0.2 +Pyruvic_acid_m+2 0.2 0.23 0.3 0.15 0.0001 0.0001 0.35 0.2 0.2 0.23 0.3 0.15 0.1 0.1 0.35 0.2 +Pyruvic_acid_m+3 0.6 0.57 0.1 0.15 0.0005 0.0005 0.25 0.3 0.6 0.57 0.1 0.15 0.1 0.1 0.25 0.3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FracContribution_C_5.csv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,26 @@ +ID MCF001089_TD01 MCF001089_TD02 MCF001089_TD07 MCF001089_TD08 MCF001089_TD19 MCF001089_TD20 MCF001089_TD25 MCF001089_TD26 MCF001089_TD37 MCF001089_TD38 MCF001089_TD43 MCF001089_TD44 MCF001089_TD55 MCF001089_TD56 MCF001089_TD61 MCF001089_TD62 +Fructose_1,6-bisphosphate 0.0 0.0 0.0 0.0 0.0 +Fumaric_acid 0.0 0.0 0.0 0.00189664357263286 0.0 0.0 0.000500041300531799 +Glycine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +Hexose 0.00762749174596484 0.00167577130357252 0.00509338901447358 0.00252875218461319 0.00575687494289638 0.00521882313638746 0.0041732481389427 0.00462441914606014 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +Hexose-phosphate 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +Ile_Leu 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Alanine 0.000300183098510707 0.0 0.0180323570915377 0.0208864367091383 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Arginine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Asparagine 0.0 0.0 0.0 0.0 0.00275043348149139 0.0 0.0 0.0 +L-Aspartic_acid 0.00711429300863751 0.00711565170397871 0.126874713735778 0.137607007753336 0.00887214703655263 0.00814181833419956 0.128546005517517 0.134463940877588 +L-Glutamic_acid 0.0186189922849795 0.0189512529072842 0.199700486213809 0.193976641844404 0.0186857662222136 0.0202828476474173 0.20124661989943 0.203786827442622 +L-Glutamine 0.00160200012909904 0.0 0.114887862236339 0.139366599094848 0.00227741586424723 0.0022177382266197 0.125412764443405 0.150842877169667 +L-Histidine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Lactic_acid 0.996169569495619 0.995975477500888 0.99592721423554 0.996105017845211 0.99599115961227 0.99599772879137 0.996132991391358 0.996246688151202 0.980373866526704 0.979007295796873 0.978534478509106 0.976787596299441 0.981176728749348 0.982344821248399 0.973048888977137 0.979345434097336 +L-Lysine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Malic_acid 3.53420625487163e-05 8.4896366324339e-05 0.00753337452964479 0.0113698929771914 0.0 0.0 0.00614506153792491 0.00843804328368624 +L-Methionine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Phenylalanine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Proline 0.00610056503723104 0.00513475924422191 0.016636816203803 0.0146250924721546 0.00333324651935455 0.00398908903111498 0.0133985852742358 0.0146846667756098 0.000911540747703803 0.00221029683948302 0.00846057868350799 0.0 0.0 0.0 0.0022582830613801 0.0 +L-Serine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Threonine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Tryptophan 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Tyrosine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Valine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +Pyruvic_acid 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 4.56717332815963e-05 0.0 0.00288745573738021 0.00271907830075352 0.00013907509437508 5.51743930058195e-05 0.00358424038619463 0.00376914936570372
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-Control-L-Cycloserine-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,25 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Glycine -1.0 1.0 1.0 cell [4.255576 3.417613] [2.87226 3.424984] +Hexose -1.0 1.0 1.0 cell [4.618336 3.491236] [2.947138 3.203724] +Hexose-phosphate -1.0 1.0 1.0 cell [4.108111 2.697149] [2.413296 2.655447] +L-Alanine -1.0 1.0 1.0 cell [3.302788 3.14283 ] [2.43315 3.200548] +L-Lysine -1.0 1.0 1.0 cell [5.576418 3.786704] [3.432559 3.499267] +L-Proline -1.0 1.0 1.0 cell [4.05992 3.613014] [2.83203 3.879342] +L-Serine -1.0 1.0 1.0 cell [5.329834 4.292357] [3.623779 4.074288] +L-Threonine -1.0 1.0 1.0 cell [4.997154 3.623269] [3.434891 3.45371 ] +Ile_Leu 1.0 1.0 1.0 cell [4.900535 3.337393] [3.030205 2.922865] +L-Arginine 1.0 1.0 1.0 cell [5.002539 3.168993] [3.358616 2.794746] +L-Aspartic_acid 1.0 1.0 1.0 cell [2.926178 0.604969] [1.310091 0.508822] +L-Glutamic_acid 1.0 1.0 1.0 cell [3.916821 2.30352 ] [2.203319 2.192284] +L-Glutamine 1.0 1.0 1.0 cell [3.10904 1.458991] [1.569472 1.216207] +L-Histidine 1.0 1.0 1.0 cell [5.046696 3.143408] [3.188606 2.910277] +L-Lactic_acid 1.0 1.0 1.0 cell [4.388836 3.17085 ] [2.580271 2.467079] +L-Malic_acid 1.0 1.0 1.0 cell [3.984239 2.221886] [3.288748 2.652708] +L-Methionine 1.0 1.0 1.0 cell [5.30659 3.77877] [3.589049 3.574521] +L-Phenylalanine 1.0 1.0 1.0 cell [4.846542 3.17885 ] [3.031899 2.794881] +L-Tryptophan 1.0 1.0 1.0 cell [4.92931 2.874653] [2.759392 2.666666] +L-Tyrosine 1.0 1.0 1.0 cell [5.003738 3.325451] [3.166826 2.956651] +L-Valine 1.0 1.0 1.0 cell [5.655527 4.449566] [4.032882 3.998557] +Pyruvic_acid 1.0 1.0 1.0 cell [1.408848 2.63986 ] [1.01521 2.037201] +Fructose_1,6-bisphosphate cell [ nan 0.71992] [nan nan] +Fumaric_acid cell [3.692766 1.743812] [2.397314 nan]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-Control-L-Cycloserine-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,20 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Hexose -1.0 1.0 1.0 med [17.323478 16.30882 ] [17.234918 19.00465 ] +Ile_Leu -1.0 1.0 1.0 med [16.69374 15.713286] [17.497952 18.300431] +L-Alanine -1.0 1.0 1.0 med [6.016043 5.722255] [6.847528 7.781428] +L-Asparagine -1.0 1.0 1.0 med [10.236824 8.224644] [ 9.877881 10.424269] +L-Histidine -1.0 1.0 1.0 med [27.655594 25.868636] [27.272808 28.447726] +L-Lactic_acid -1.0 1.0 1.0 med [25.499578 24.518913] [24.102561 26.366482] +L-Methionine -1.0 1.0 1.0 med [17.685546 16.454068] [18.42993 18.993209] +L-Phenylalanine -1.0 1.0 1.0 med [16.550902 15.608278] [17.382841 18.270953] +L-Proline -1.0 1.0 1.0 med [3.778766 2.810272] [4.090356 5.553318] +L-Serine -1.0 1.0 1.0 med [18.049649 16.621876] [18.097065 19.327089] +L-Threonine -1.0 1.0 1.0 med [23.81829 22.118877] [24.1371 24.713005] +L-Tyrosine -1.0 1.0 1.0 med [18.565282 17.161201] [18.880702 19.863464] +L-Valine -1.0 1.0 1.0 med [22.789674 21.740482] [23.848366 24.293696] +Glycine 1.0 1.0 1.0 med [4.11994 3.84192] [5.444741 4.334016] +Hexose-phosphate 1.0 1.0 1.0 med [7.225669 5.373172] [8.029712 6.894561] +L-Arginine 1.0 1.0 1.0 med [52.762527 50.409341] [52.519447 51.499051] +L-Lysine 1.0 1.0 1.0 med [68.280981 66.313756] [68.367814 67.499031] +L-Tryptophan 1.0 1.0 1.0 med [14.618856 12.939212] [13.272943 12.897328] +Pyruvic_acid 1.0 1.0 1.0 med [26.166366 26.254509] [27.261571 27.575891]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example5_metadata.csv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,17 @@ +name_to_plot condition timepoint timenum compartment original_name +Ctrl_cell_T0-1 Control T0 0 cell MCF001089_TD01 +Ctrl_cell_T0-2 Control T0 0 cell MCF001089_TD02 +Ctrl_cell_T2h-1 Control T2h 2 cell MCF001089_TD07 +Ctrl_cell_T2h-2 Control T2h 2 cell MCF001089_TD08 +L-Cyc_cell_T0-1 L-Cycloserine T0 0 cell MCF001089_TD19 +L-Cyc_cell_T0-2 L-Cycloserine T0 0 cell MCF001089_TD20 +L-Cyc_cell_T2h-1 L-Cycloserine T2h 2 cell MCF001089_TD25 +L-Cyc_cell_T2h-2 L-Cycloserine T2h 2 cell MCF001089_TD26 +Ctrl_med_T0-1 Control T0 0 med MCF001089_TD37 +Ctrl_med_T0-2 Control T0 0 med MCF001089_TD38 +Ctrl_med_T2h-1 Control T2h 2 med MCF001089_TD43 +Ctrl_med_T2h-2 Control T2h 2 med MCF001089_TD44 +L-Cyc_med_T0-1 L-Cycloserine T0 0 med MCF001089_TD55 +L-Cyc_med_T0-2 L-Cycloserine T0 0 med MCF001089_TD56 +L-Cyc_med_T2h-1 L-Cycloserine T2h 2 med MCF001089_TD61 +L-Cyc_med_T2h-2 L-Cycloserine T2h 2 med MCF001089_TD62
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--cell--MDV-Control-L-Cycloserine--T0-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,11 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +L-Arginine -0.979871 0.000109 0.001092 cell [0.07 0.06 0.05 0.04 0.03 0.02 0.0001] [0.0001 0.02 0.03 0.04 0.05 0.06 0.07 ] +Glycine -0.973056 0.148117 0.493723 cell [0.5 0.2 0.001] [0.001 0.2 0.5 ] +L-Glutamic_acid -0.739657 0.092845 0.464226 cell [0.5 0.23 0.13 0.1 0.04 0.001] [0.001 0.04 0.1 0.13 0.23 0.5 ] +Pyruvic_acid -0.67551 0.32449 0.657105 cell [0.074833 0.1249 0.214476 0.584808] [5.84808e-01 2.14476e-01 1.00000e-04 5.00000e-04] +L-Alanine -0.671448 0.328552 0.657105 cell [7.34166e-01 2.62679e-01 1.00000e-02 1.00000e-04] [1.00e-04 1.00e-02 2.11e-01 6.99e-01] +L-Lactic_acid -0.344007 0.655993 0.937133 cell [1.0000e-04 1.0000e-04 1.1796e-02 9.8820e-01] [9.8805e-01 1.1947e-02 1.0000e-04 1.0000e-04] +L-Aspartic_acid -0.278038 0.650607 0.937133 cell [9.8645e-01 2.0000e-04 1.2380e-02 1.1310e-03 1.0000e-04] [3.16000e-04 1.71500e-03 1.49730e-02 1.89737e-01 1.00000e-04] +Fructose_1,6-bisphosphate cell [nan nan nan nan nan nan nan] [nan nan nan nan nan nan nan] +Fumaric_acid cell [nan nan nan nan nan] [ nan nan nan nan 0.000387] +L-Glutamine cell [nan nan nan nan nan nan] [2.82843e-01 5.83100e-03 9.67500e-03 1.00000e-04 6.00000e-03 2.00000e-03]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--cell--MDV-Control-L-Cycloserine--T2h-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,11 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.407405 0.592595 1.0 cell [0.244949 0.424264 0.212132 0.122474] [0.054772 0.173205 0.264575 0.273861] +L-Lactic_acid -0.344007 0.655993 1.0 cell [9.8805e-01 1.1947e-02 1.0000e-04 1.0000e-04] [1.0000e-04 1.0000e-04 1.1796e-02 9.8820e-01] +Glycine -0.187368 0.880008 1.0 cell [0.273861 0.574456 0.003162] [0.004472 0.387298 0.5 ] +L-Arginine 0.645497 0.117387 0.293467 cell [1.e-04 1.e-04 1.e-04 1.e+00 1.e-04 1.e-04 1.e-04] [0.0001 0.01 0.0001 0.01 0.0001 0.0001 0.0001] +L-Alanine 0.932835 0.067165 0.223885 cell [1.00e+00 1.00e-04 1.41e-04 6.16e-03] [7.34166e-01 2.62679e-01 1.00000e-04 1.00000e-04] +L-Aspartic_acid 0.99977 4e-06 2.1e-05 cell [0.737613 0.070846 0.125771 0.056138 0.009165] [0.747988 0.06325 0.116466 0.059249 0.012935] +L-Glutamic_acid 0.999941 0.0 0.0 cell [0.564508 0.071156 0.246995 0.059399 0.048197 0.009499] [0.556649 0.070137 0.249195 0.06265 0.0507 0.010588] +Fructose_1,6-bisphosphate cell [0.01 0.0001 0.0001 0.0001 0.01 0.0001 0.0001] [ nan 0.000316 nan nan 0.01 nan nan] +Fumaric_acid cell [9.98949e-01 1.00000e-04 6.56000e-04 2.45000e-04 4.00000e-04] [nan nan nan nan nan] +L-Glutamine cell [nan nan nan nan nan nan] [nan nan nan nan nan nan]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--cell--MDV-T2h-T0--Control-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,11 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.710557 0.289443 0.723607 cell [0.244949 0.424264 0.212132 0.122474] [0.074833 0.1249 0.214476 0.584808] +L-Lactic_acid -0.344007 0.655993 1.0 cell [9.8805e-01 1.1947e-02 1.0000e-04 1.0000e-04] [1.0000e-04 1.0000e-04 1.1796e-02 9.8820e-01] +L-Arginine 0.025903 0.956041 1.0 cell [1.e-04 1.e-04 1.e-04 1.e+00 1.e-04 1.e-04 1.e-04] [0.07 0.06 0.05 0.04 0.03 0.02 0.0001] +Glycine 0.368192 0.759953 1.0 cell [0.273861 0.574456 0.003162] [0.5 0.2 0.001] +L-Glutamic_acid 0.895139 0.015917 0.079587 cell [0.564508 0.071156 0.246995 0.059399 0.048197 0.009499] [0.5 0.23 0.13 0.1 0.04 0.001] +L-Alanine 0.934368 0.065632 0.218775 cell [1.00e+00 1.00e-04 1.41e-04 6.16e-03] [7.34166e-01 2.62679e-01 1.00000e-02 1.00000e-04] +L-Aspartic_acid 0.99186 0.00088 0.008805 cell [0.737613 0.070846 0.125771 0.056138 0.009165] [9.8645e-01 2.0000e-04 1.2380e-02 1.1310e-03 1.0000e-04] +Fructose_1,6-bisphosphate cell [0.01 0.0001 0.0001 0.0001 0.01 0.0001 0.0001] [nan nan nan nan nan nan nan] +Fumaric_acid cell [9.98949e-01 1.00000e-04 6.56000e-04 2.45000e-04 4.00000e-04] [nan nan nan nan nan] +L-Glutamine cell [nan nan nan nan nan nan] [nan nan nan nan nan nan]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--cell--MDV-T2h-T0--L-Cycloserine-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,11 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.995621 0.004379 0.043786 cell [0.054772 0.173205 0.264575 0.273861] [5.84808e-01 2.14476e-01 1.00000e-04 5.00000e-04] +L-Alanine -0.666339 0.333661 0.834151 cell [7.34166e-01 2.62679e-01 1.00000e-04 1.00000e-04] [1.00e-04 1.00e-02 2.11e-01 6.99e-01] +L-Glutamic_acid -0.600809 0.207224 0.834151 cell [0.556649 0.070137 0.249195 0.06265 0.0507 0.010588] [0.001 0.04 0.1 0.13 0.23 0.5 ] +L-Lactic_acid -0.344007 0.655993 0.938087 cell [1.0000e-04 1.0000e-04 1.1796e-02 9.8820e-01] [9.8805e-01 1.1947e-02 1.0000e-04 1.0000e-04] +L-Aspartic_acid -0.273092 0.656661 0.938087 cell [0.747988 0.06325 0.116466 0.059249 0.012935] [3.16000e-04 1.71500e-03 1.49730e-02 1.89737e-01 1.00000e-04] +L-Arginine -0.243607 0.598601 0.938087 cell [0.0001 0.01 0.0001 0.01 0.0001 0.0001 0.0001] [0.0001 0.02 0.03 0.04 0.05 0.06 0.07 ] +Glycine 0.912581 0.268172 0.834151 cell [0.004472 0.387298 0.5 ] [0.001 0.2 0.5 ] +Fructose_1,6-bisphosphate cell [ nan 0.000316 nan nan 0.01 nan nan] [nan nan nan nan nan nan nan] +Fumaric_acid cell [nan nan nan nan nan] [ nan nan nan nan 0.000387] +L-Glutamine cell [nan nan nan nan nan nan] [2.82843e-01 5.83100e-03 9.67500e-03 1.00000e-04 6.00000e-03 2.00000e-03]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--med--MDV-Control-L-Cycloserine--T0-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,6 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.566976 0.433024 0.855516 med [0.1 0.1 0.214476 0.584808] [0.584808 0.214476 0.1 0.1 ] +L-Arginine 0.3 0.51331 0.855516 med [0.01 0.0001 0.0001 0.01 0.0001 0.0001 0.0001] [0.0001 0.0001 0.01 0.01 0.0001 0.0001 0.0001] +L-Lactic_acid 0.999998 2e-06 1e-05 med [1.6137e-02 2.0000e-04 1.2050e-02 9.7160e-01] [1.4087e-02 2.0000e-04 1.2050e-02 9.7365e-01] +Glycine med [nan nan nan] [nan nan nan] +L-Alanine med [0.0001] [0.0001]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--med--MDV-Control-L-Cycloserine--T2h-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,6 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.407405 0.592595 0.987658 med [0.244949 0.424264 0.212132 0.122474] [0.054772 0.173205 0.264575 0.273861] +L-Arginine 0.645497 0.117387 0.293467 med [1.e-04 1.e-04 1.e-04 1.e+00 1.e-04 1.e-04 1.e-04] [0.0001 0.01 0.0001 0.01 0.0001 0.0001 0.0001] +L-Lactic_acid 0.999999 1e-06 5e-06 med [1.8178e-02 2.0000e-04 1.2050e-02 9.6955e-01] [1.94380e-02 1.41000e-04 1.18500e-02 9.68195e-01] +Glycine med [nan nan nan] [nan nan nan] +L-Alanine med [0.000608] [0.0001]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--med--MDV-T2h-T0--Control-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,6 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.764727 0.235273 0.392122 med [0.244949 0.424264 0.212132 0.122474] [0.1 0.1 0.214476 0.584808] +L-Arginine 0.645497 0.117387 0.293467 med [1.e-04 1.e-04 1.e-04 1.e+00 1.e-04 1.e-04 1.e-04] [0.01 0.0001 0.0001 0.01 0.0001 0.0001 0.0001] +L-Lactic_acid 0.999998 2e-06 1e-05 med [1.8178e-02 2.0000e-04 1.2050e-02 9.6955e-01] [1.6137e-02 2.0000e-04 1.2050e-02 9.7160e-01] +Glycine med [nan nan nan] [nan nan nan] +L-Alanine med [0.000608] [0.0001]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--med--MDV-T2h-T0--L-Cycloserine-pearson.tsv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,6 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.974457 0.025543 0.063858 med [0.054772 0.173205 0.264575 0.273861] [0.584808 0.214476 0.1 0.1 ] +L-Arginine 0.3 0.51331 0.855516 med [0.0001 0.01 0.0001 0.01 0.0001 0.0001 0.0001] [0.0001 0.0001 0.01 0.01 0.0001 0.0001 0.0001] +L-Lactic_acid 0.999985 1.5e-05 7.4e-05 med [1.94380e-02 1.41000e-04 1.18500e-02 9.68195e-01] [1.4087e-02 2.0000e-04 1.2050e-02 9.7365e-01] +Glycine med [nan nan nan] [nan nan nan] +L-Alanine med [0.0001] [0.0001]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rawAbundances_5.csv Thu Feb 15 12:50:27 2024 +0000 @@ -0,0 +1,26 @@ +ID MCF001089_TD01 MCF001089_TD02 MCF001089_TD07 MCF001089_TD08 MCF001089_TD19 MCF001089_TD20 MCF001089_TD25 MCF001089_TD26 MCF001089_TD37 MCF001089_TD38 MCF001089_TD43 MCF001089_TD44 MCF001089_TD55 MCF001089_TD56 MCF001089_TD61 MCF001089_TD62 +Fructose_1,6-bisphosphate 81.46798666666666 31.66305777777778 488.62223666666665 30.88032133333333 108.58193666666666 +Fumaric_acid 1765.8621555555562 2350.101706666667 565.6100944444463 1636.1451616666689 1112.7411533333332 1571.7939723809532 2082.227511666667 +Glycine 31339.848144444444 19953.502358333335 15011.070372222222 26867.879408333334 20173.435886666666 14121.041376190477 15741.494772222224 25731.819858333336 21082398.016666666 20528546.116666667 19650482.416666664 19152242.516666666 35768152.41666667 21132662.81666667 21540901.71666667 22233782.916666664 +Hexose 15263.525582222223 10653.204421666667 7620.2662477777785 12194.176071666667 9284.639177333334 7131.811518095239 6702.562494444444 11674.364736666666 23812934.643333334 24242428.643333334 22336054.643333334 22906432.643333334 23957348.643333334 23850557.643333334 26889340.643333334 25837975.643333334 +Hexose-phosphate 556790.6730444445 410704.96478333336 215369.08985555556 457681.9897833334 337548.2038266667 233788.3998761905 229354.86985555556 416586.1147833334 1792538.5666666667 1790949.5666666667 1218328.5666666667 1457111.5666666667 2069691.5666666667 1915534.5666666667 1684708.5666666667 1734938.5666666667 +Ile_Leu 723695.6614222223 871117.5290666667 433211.3440444445 674932.9420666667 545783.4088533333 441641.19203809527 354037.3863777778 633452.6395666667 2111708660.1333334 2203285239.133333 2037012929.1333334 2023660803.1333334 2311992779.133333 2210982973.133333 2389754947.133333 2339735205.133333 +L-Alanine 14581.8738 7816.563399999999 7056.1678999999995 14626.51065 9781.123839999998 6324.36291142857 8061.856666666667 13276.4346 1548485.77 1701510.73 1309197.7400000002 1820745.4700000002 1935085.62 1763954.77 1931224.9000000004 2282473.1300000004 +L-Arginine 5680.366466666666 7466.331200000001 4182.386200000001 4069.3133000000003 5139.229840000001 3719.8487428571434 2943.6414666666674 4496.78815 76704557.1 76562817.1 74284491.1 72162535.1 76269336.1 76291863.1 74652772.1 74944609.1 +L-Asparagine 3617749.87 3435790.2 2756887.13 2910381.68 3513705.7 3293797.9 3311566.8 3892175.2 +L-Aspartic_acid 71486.78267333333 55376.312 8361.739503333332 20235.678005 34321.611392 23119.754611428572 7664.626003333333 15616.709855000001 +L-Glutamic_acid 139191.37992666668 104355.48684499999 46972.50566333334 106954.896995 82261.28531600001 55875.258682857144 47872.660330000006 95053.066995 +L-Glutamine 18606.32958888889 9863.261441666667 4512.041427777778 8956.960391666667 8701.497033333335 5374.547080952381 4094.7460777777783 6858.299791666668 +L-Histidine 16420.387355555555 15111.119316666667 8215.772844444444 11717.067916666667 12255.282253333333 8082.469038095238 7269.836411111111 11350.365116666668 66137818.63333333 67607708.63333334 63420421.63333333 61687625.63333333 64943662.63333333 66958084.63333333 67970373.63333334 69607422.63333334 +L-Lactic_acid 1073607.0293955556 1722584.2720466666 973301.2546977778 991816.0770466666 879872.2496373333 726504.4068838095 614361.0746977777 951194.5220466666 9322737799.093334 9302697744.093334 9196079213.093334 8719390692.093334 8901197393.093334 8704911808.093334 9400722189.093334 9863466762.093334 +L-Lysine 11537.73680888889 13806.366056666666 8333.777904444445 8813.939856666668 9173.407525333334 6579.528718095239 6643.038094444445 9442.279106666667 117443154.71333334 121027940.71333334 115723826.71333334 115850611.09333333 119744345.59333333 119004184.71333334 118584270.71333334 117133694.71333334 +L-Malic_acid 83435.18658666659 84111.08978999997 28512.006359999974 76546.89803999996 79766.01795199995 59945.28643999999 37016.17602666664 84042.47953999996 +L-Methionine 50953.09172444445 49086.99679333334 28047.987862222224 45217.35266333333 38660.34303466667 29593.68731047619 25367.68152888889 44736.38582833333 111550662.21666667 114041484.58666667 102236906.58666667 107705253.05666667 118873593.96666667 116214414.89666668 118851523.58666667 123449681.58666667 +L-Phenylalanine 246751.26231111115 294311.09893333336 140657.68205555558 222115.47443333335 189439.93394666666 150023.76081904763 115791.1377888889 208570.64043333335 636990553.8666667 649933157.8666667 607515203.8666667 606053781.8666667 685784788.8666667 665904616.8666667 714741480.8666667 705881485.8666667 +L-Proline 6399.387268888889 4826.820016666667 3510.949071111111 6967.536411666666 4196.610013333333 3581.472580952381 4106.875117777778 6867.035166666667 6433495.033333333 6609824.833333334 5540393.533333333 4245151.533333333 7152407.533333333 6966378.033333333 9268074.033333333 9909521.833333334 +L-Serine 34591.22677111111 27843.714578333333 20292.688385555557 30783.493578333335 24105.163262666665 18470.518616190475 18382.152052222224 30617.729578333332 85713015.15666667 86442185.15666667 80830195.15666667 77735867.15666667 87723164.15666667 84905739.15666667 90456917.15666667 93913089.15666667 +L-Threonine 162184.6072 122218.556075 79915.61493 130398.02227 113231.489568 82710.40769142858 75580.73975333333 125274.2576 285717399.29 278341478.49 261018102.39 262753775.69 287841134.94 283733608.09 296904540.79 288355169.29 +L-Tryptophan 4101.068422222223 4813.902566666667 2571.5729777777774 2610.923316666667 2975.5369333333333 2079.1386666666667 2157.056777777778 2678.538611666667 23656601.733333334 24177093.733333334 23401859.733333334 19146747.733333334 22572464.733333334 20887438.733333334 20532655.733333334 21681238.733333334 +L-Tyrosine 216327.26993777775 233028.43495333332 117722.98240222223 189134.5396533333 158752.20572266664 127191.96683047619 98779.61883555555 178181.92245333333 526242843.90666664 541860987.9066666 489041215.90666664 498219681.90666664 554116402.9066666 532238404.90666664 568375310.9066666 574309133.9066666 +L-Valine 204800.46126444443 179839.41518833334 124299.92819888888 183414.65549833333 153570.35555866666 121953.23554190475 102920.69711555555 178884.87684833334 577225423.9966667 578990937.1966666 545903388.7966666 557138987.7966666 606569154.8966666 603361959.6966666 611454433.5966667 621103613.1966666 +Pyruvic_acid 629.5377555555556 1468.3793166666667 1214.9325444444444 2671.4148166666664 750.1246533333333 639.8964666666667 960.6392111111111 2012.0523166666667 1917193228.8333335 1800847679.2333333 1898133517.2333333 1831205498.1333334 1954504808.4333334 1917436849.8333335 1873057071.1333334 2047218329.5333335