Mercurial > repos > iuc > dimet_bivariate_analysis
changeset 0:89e637c99bed draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dimet_bivariate_analysis.xml Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,275 @@ +<tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description> + Computation of the correlation of MDV profiles, or the metabolite time course profiles (by DIMet) + </description> + <macros> + <token name="@TOOL_LABEL@">bivariate analysis</token> + <token name="@EXECUTABLE@">bivariate_analysis</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + @INIT_CONFIG@ + @INIT_BI_ANALYSIS@ + @INIT_BIVAR_COMPARISONS@ + HYDRA_FULL_ERROR=1 python -m dimet + -cp '$__new_file_path__/config' + '++hydra.run.dir=bivariate_analysis' + '++figure_path=figures' + '++table_path=tables' + '++analysis={ + dataset:{ + _target_: dimet.data.DatasetConfig, + name: "I am a synthetic data example" + }, + method:{ + _target_: dimet.method.BivariateAnalysisConfig, + label: "bivariate analysis", + name: "Computation of the correlation of MDV profiles, or the metabolite time course profiles" + }, + label: bivariate-analysis-example2 + }' + '++analysis.conditions=${conditions}' + '++analysis.dataset.label=' + '++analysis.method.correction_method=${correction_method}' + '++analysis.method.impute_values=${impute_values}' + '++analysis.method.conditions_metabolite_time_profiles=${conditions_metabolite_time_profiles}' + '++analysis.method.timepoints_MDV_comparison=${timepoints_MDV_comparison}' + '++analysis.method.conditions_MDV_comparison=${conditions_MDV_comparison}' + '++analysis.method.output_include_gmean_arr_columns=true' + '++analysis.dataset.subfolder=' + '++analysis.dataset.conditions=${conditions}' + #if $metadata_path: + '++analysis.dataset.metadata=metadata' + #end if + #if str( $data_input.data_input_selector ) == "abundance": + #if $data_input.abundance_file: + '++analysis.dataset.abundances=abundance' + #end if + #elif str( $data_input.data_input_selector ) == "mean_enrichment": + #if $data_input.me_or_frac_contrib_file: + '++analysis.dataset.mean_enrichment=me_or_frac_contrib' + #end if + #elif str( $data_input.data_input_selector ) == "isotop_prop": + #if $data_input.isotop_prop_file: + '++analysis.dataset.isotopologue_proportions=isotop_prop' + #end if + #else + #if $data_input.isotop_abs_file: + '++analysis.dataset.isotopologues=isotop_abs' + #end if + #end if + @REMOVE_CONFIG@ + ]]></command> + <inputs> + <expand macro="input_parameters_bivar_analysis"/> + <expand macro="plot_factor_list"/> + <expand macro="correction_method"/> + </inputs> + + <outputs> + <collection name="report" type="list"> + <discover_datasets pattern="__designation__" directory="tables" format="tabular"/> + </collection> + </outputs> + <tests> + <test> + <param name="data_input_selector" value="isotop_prop" /> + <param name="isotop_prop_file" ftype="tabular" value="CorrectedIsotopologues_5.csv"/> + <param name="metadata_path" ftype="tabular" value="example5_metadata.csv"/> + <param name="correction_method" value="fdr_bh"/> + <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="8"> + <element file="isotop_prop--cell--MDV-Control-L-Cycloserine--T0-pearson.tsv" name="isotop_prop--cell--MDV-Control-L-Cycloserine--T0-pearson.tsv" ftype="tabular"/> + <element file="isotop_prop--cell--MDV-Control-L-Cycloserine--T2h-pearson.tsv" name="isotop_prop--cell--MDV-Control-L-Cycloserine--T2h-pearson.tsv" ftype="tabular"/> + <element file="isotop_prop--cell--MDV-T2h-T0--Control-pearson.tsv" name="isotop_prop--cell--MDV-T2h-T0--Control-pearson.tsv" ftype="tabular"/> + <element file="isotop_prop--cell--MDV-T2h-T0--L-Cycloserine-pearson.tsv" name="isotop_prop--cell--MDV-T2h-T0--L-Cycloserine-pearson.tsv" ftype="tabular"/> + <element file="isotop_prop--med--MDV-Control-L-Cycloserine--T0-pearson.tsv" name="isotop_prop--med--MDV-Control-L-Cycloserine--T0-pearson.tsv" ftype="tabular"/> + <element file="isotop_prop--med--MDV-Control-L-Cycloserine--T2h-pearson.tsv" name="isotop_prop--med--MDV-Control-L-Cycloserine--T2h-pearson.tsv" ftype="tabular"/> + <element file="isotop_prop--med--MDV-T2h-T0--Control-pearson.tsv" name="isotop_prop--med--MDV-T2h-T0--Control-pearson.tsv" ftype="tabular"/> + <element file="isotop_prop--med--MDV-T2h-T0--L-Cycloserine-pearson.tsv" name="isotop_prop--med--MDV-T2h-T0--L-Cycloserine-pearson.tsv" ftype="tabular"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ + +This module is part of DIMet: Computation of the correlation of entire MDV profiles, or the metabolite time course profiles (https://pypi.org/project/DIMet/). + +DIMet bi-variate analysis performs the comparison of entire MDV profiles, with the user provided isotopologue proportions data. Moreover, when total abundances and/or mean enrichment are provided, the comparison of the metabolite time-course profiles is also computed. Specifically, three types of bi-variate comparisons are performed automatically: + + +- MDV profile comparison between two conditions + +- MDV profile comparison between two consecutive time-points + +- Metabolite (total abundances and/or mean enrichment) time course profiles comparison between two conditions + + +For all these three types of bi-variate comparison, the statistical test that is applied is the Pearson's correlation test. + + +To note, MDV (Mass Distribution Vector) are obtained automatically by the tool, using the isotopologue proportions. + + + + **Input data files** + +This tool requires (at max.) 4 tab-delimited .csv files as inputs. There are two types of files: + +- The measures' (or quantifications') files, that can be of 3 types. + +- The metadata, a unique file with the description of the samples in your measures' files. This is compulsory. + +For running DIMet @EXECUTABLE@ you need **at least one file** of measures: + +- The **isotopologue proportions** file + +- The total **abundances** (of the metabolites) file + +- The mean **enrichment** or labelled fractional contributions + + +and one metadata file, WHICH IS COMPULSORY, see section **Metadata File Information**. + + +**Measures files** + +The measures files must be organized as matrices: + +- The first column must contain Metabolite IDs that are unique (not repeated) within the file. + +- The rest of the columns correspond to the samples + +- The rows correspond to the metabolites + +- The values must be tab separated, with the first row containing the sample/column labels. + +See the following examples of measures files: + + +Example - Metabolites **abundances**: + + =============== ================== ================== ================== ================== ================== ================== + ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06** + =============== ================== ================== ================== ================== ================== ================== + 2_3-PG 8698823.9926 10718737.7217 10724373.9 8536484.5 22060650 28898956 + 2-OHGLu 36924336 424336 92060650 45165 84951950 965165051 + Glc6P 2310 2142 2683 1683 012532068 1252172 + Gly3P 399298 991656565 525195 6365231 89451625 4952651963 + IsoCit 0 0 0 84915613 856236 954651610 + =============== ================== ================== ================== ================== ================== ================== + +Example - mean **enrichment** or labeled fractional contributions: + + =============== ================== ================== ================== ================== ================== ================== + ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06** + =============== ================== ================== ================== ================== ================== ================== + 2_3-PG 0.9711 0.968 0.9909 0.991 0.40 0.9 + 2-OHGLu 0.01719 0.0246 0.554 0.555 0.73 0.68 + Glc6P 0.06 0.66 2683 0.06 2068 2172 + Gly3P 0.06 0.06 0.06 1 5 3 + IsoCit 0.06 1 0.49 0.36 6 10 + =============== ================== ================== ================== ================== ================== ================== + + + +Example - **Isotopologue proportions**: + + =============== ================== ================== ================== ================== ================== ================== + ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06** + =============== ================== ================== ================== ================== ================== ================== + 2_3-PG_m+0 0.023701408 0.026667837 0.003395407 0.05955 0.034383527 0.12 + 2_3-PG_m+1 0.0 0.0 0.0 0.0 0.4 0.12 + 2_3-PG_m+2 0.015379329 0.01506 0.017029723 0.35483229 0.54131313 0.743 + 2_3-PG_m+3 0.960919263 0.958268099 0.97957487 0.581310816 0.017029723 0.017 + 2-OHGLu_m+0 0.972778716 0.960016157 0.238843937 0.234383527 0.9998888 0.015064063 + 2-OHGLu_m+1 0.0 0.0 0.0 0.0 0.0001112 0.960919263 + =============== ================== ================== ================== ================== ================== ================== + + + +**Metadata File Information** + +Provide a tab-separated file that has the names of the samples in the first column and one header row. +Column names must be exactly in this order: + + name_to_plot + condition + timepoint + timenum + compartment + original_name + + +Example **Metadata File**: + + + ==================== =============== ============= ============ ================ ================= + **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name** + -------------------- --------------- ------------- ------------ ---------------- ----------------- + Control_cell_T0-1 Control T0 0 cell MCF001089_TD01 + Control_cell_T0-2 Control T0 0 cell MCF001089_TD02 + Control_cell_T0-3 Control T0 0 cell MCF001089_TD03 + Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04 + Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05 + Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06 + Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07 + Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08 + Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01 + Control_med_T24-1 Control T24 24 med MCF001090_TD02 + Control_med_T24-2 Control T24 24 med MCF001090_TD03 + Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04 + Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05 + Control_med_T0-1 Control T0 0 med MCF001090_TD06 + Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07 + Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08 + ==================== =============== ============= ============ ================ ================= + + +The column **original_name** must have the names of the samples as given in your data. + +The column **name_to_plot** must have the names as you want them to be (or set identical to original_name if you prefer). To set names that +are meaningful is a better choice, as we will take them to display the results. + +The column **timenum** must contain only the numeric part of the timepoint, for example 2,0, 10, 100 (this means, without letters ("T", "t", "s", "h" etc) +nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!). + +The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the +compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column. + + +**Running the analysis** + +You can precise how you want your analysis to be executed, with the parameters: + +- **datatypes** : the measures type(s) that you want to run. + +- **conditions**: the two conditions to be compared in the bi-variate analysis. If 3 or more conditions are set, the tool automatically performs all the 1-to-1 condition comparisons. If you only have one condition in your data, select the condition, and see the Note at the end of this section. + +- **correction_method** : one of the methods for multiple testing correction available in statsmodels library (bonferroni, fdr_bh, sidak, among others, see https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html). + + +**Note**: the tool automatically performs the comparison of *MDV profile between two consecutive time-points*. All the time-points are processed. + + +There exist hints on use that will guide you, next to the parameters. + +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/records/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/records/10579891 + + ]]> + </help> + <expand macro="citations" /> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,1108 @@ +<macros> + <token name="@TOOL_VERSION@">0.2.1</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@EXECUTABLE@">pca</token> + <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"> + <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> + <citation type="bibtex"> + @software{Galvis_Rodriguez_DIMet, + author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha}, + license = {MIT}, + title = {{DIMet}}, + url = {https://github.com/cbib/DIMet} + } + + </citation> + </citations> + + </xml> + <xml name="metadata_file_macros"> + <param name="metadata_path" type="data" format="tabular" label="metadata file" help="The metadata, a unique file with the description of the samples in your measures' files. This is compulsory, see section Metadata File Information."/> + </xml> + <xml name="abundance_file_macros"> + <param name="abundance_file" type="data" format="tabular" label="Metabolite abundance file" help="The total abundances file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples - The rows correspond to the metabolites - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/> + </xml> + <xml name="enrichment_file_macros"> + <param name="me_or_frac_contrib_file" type="data" format="tabular" label="Metabolite enrichment file" help="The mean enrichment file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the metabolites. - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/> + </xml> + <xml name="isotopologue_prop_file_macros"> + <param name="isotop_prop_file" type="data" format="tabular" label="Isotopologues proportion abundance file" help=" The isotopologue proportions file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/> + </xml> + <xml name="isotopologue_abs_file_macros"> + <param name="isotop_abs_file" type="data" format="tabular" label="Isotopologues absolute abundance file" help="The isotopologue absolute values file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/> + </xml> + <xml name="input_parameters_pca"> + <expand macro="abundance_file_macros"/> + <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/> + <expand macro="metadata_file_macros"/> + </xml> + <xml name="input_parameters_abundance"> + <expand macro="abundance_file_macros"/> + <expand macro="metadata_file_macros"/> + </xml> + <xml name="input_parameters_enrichment"> + <expand macro="enrichment_file_macros"/> + <expand macro="metadata_file_macros"/> + </xml> + <xml name="input_parameters_isotopologue"> + <expand macro="isotopologue_prop_file_macros"/> + <expand macro="metadata_file_macros"/> + </xml> + <xml name="input_parameters_metabologram"> + <conditional name="data_input"> + <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 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"/> + <column name="value" index="0"/> + <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> + <filter type="remove_value" value="metabolite_or_isotopologue"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <expand macro="statistical_test"/> + </when> + <when value="mean_enrichment"> + <expand macro="enrichment_file_macros"/> + <param name="metabolites_list" type="select" optional="false" multiple="true" + 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"/> + <column name="value" index="0"/> + <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> + <filter type="remove_value" value="metabolite_or_isotopologue"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <expand macro="statistical_test"/> + </when> + </conditional> + <param name="path_kegg_metabolites" type="data" format="tabular" label="Pathways kegg metabolites file" help="A file with the pathways and respective metabolites ID, that must match with those in your metabolomics 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)"/> + <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 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"/> + + </when> + <when value="mean_enrichment"> + <expand macro="enrichment_file_macros"/> + <expand macro="statistical_test"/> + </when> + <when value="isotop_prop"> + <expand macro="isotopologue_prop_file_macros"/> + <expand macro="statistical_test"/> + </when> + <when value="isotop_abs"> + <expand macro="isotopologue_abs_file_macros"/> + <expand macro="statistical_test"/> + </when> + </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=""> + <valid initial="string.ascii_letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + </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 condition list"> + <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> + </xml> + <xml name="conditions_multigroup"> + <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file. (1 min. only if three timepoints are set). You have to load a metadata file prior to have access to conditions"> + <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> + </xml> + <xml name="timepoint_multigroup"> + <param name="timepoint" type="select" optional="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if three conditions are set). You have to load a metadata file prior to have access to conditions"> + <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> + </xml> + <xml name="timepoint"> + <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"/> + <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> + </xml> + <xml name="grouping"> + <param name="grouping" type="select" optional="false" multiple="true" label="Browse group to compare"> + <option value="condition" selected="true">condition</option> + <option value="timepoint" selected="true">timepoint</option> + </param> + </xml> + <xml name="correction_method"> + <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method"> + <option value="bonferroni">bonferroni</option> + <option value="holm-sidak">holm-sidak</option> + <option value="holm">holm</option> + <option value="simes-hochberg">simes-hochberg</option> + <option value="hommel">hommel</option> + <option value="fdr_bh">fdr_bh</option> + <option value="fdr_by">fdr_by</option> + <option value="fdr_tsbh">fdr_tsbh</option> + <option value="fdr_tsbky">fdr_tsbky</option> + </param> + </xml> + <xml name="compartments_enrichment"> + <param name="compartments" type="select" optional="false" multiple="true" + label="Browse compartments from metadata file (All needed). 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_abundance"> + <param name="compartments" type="select" optional="false" multiple="true" + label="Browse compartments from metadata file (All needed). 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_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"> + <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="abundance_metabolites_list"> + <param name="metabolites_list" type="select" optional="false" multiple="true" + 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"/> + <column name="value" index="0"/> + <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> + <filter type="remove_value" value="metabolite_or_isotopologue"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </xml> + <xml name="enrichment_metabolites_list"> + <param name="metabolites_list" type="select" optional="false" multiple="true" + 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"/> + <filter type="unique_value" name="ID" column="0"/> + <filter type="remove_value" value="ID"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </xml> + <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 min 1 metabolite"/> + <options from_dataset="isotop_prop_file"> + <column name="ID" index="0"/> + <column name="value" index="0"/> + <filter type="unique_value" name="ID" column="0"/> + <filter type="remove_value" value="ID"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="\t"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </xml> + <xml name="deg_list"> + <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 && + + #if $metadata_path: + ln -s '$metadata_path' data/metadata.csv && + #end if + #if $abundance_file: + ln -s '$abundance_file' data/abundance.csv && + #end if + #if $me_or_frac_contrib_file: + ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && + #end if + + ]]></token> + <token name="@INIT_CONFIG@"><![CDATA[ + mkdir -p '$__new_file_path__/config' && + touch '$__new_file_path__/config/config.yaml' && + ]]></token> + <token name="@REMOVE_CONFIG@"><![CDATA[ + && rm -r '$__new_file_path__/config' + ]]></token> + <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[ + + mkdir -p data && + + #if $metadata_path: + ln -s '$metadata_path' data/metadata.csv && + #end if + #if $abundance_file: + ln -s '$abundance_file' data/abundance.csv && + #end if + ]]></token> + <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[ + + mkdir -p data && + + #if $metadata_path: + ln -s '$metadata_path' data/metadata.csv && + #end if + #if $me_or_frac_contrib_file: + ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && + #end if + ]]></token> + <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[ + + mkdir -p data && + + #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/metadata.csv && + #end if + #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 && + + #if $metadata_path: + ln -s '$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/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_METABOLOGRAM@"><![CDATA[ + #import json + #import re + #import os + #import csv + #import subprocess + + mkdir -p data && + + #if $path_kegg_metabolites: + ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv && + #end if + #if $path_kegg_transcripts: + ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv && + #end if + + #if $metadata_path: + ln -s '$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/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/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 '${s.input}' data/DEG_comparison'${cpt}'.csv && + #end for + + + ]]></token> + <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[ + + mkdir -p data && + + #if $metadata_path: + ln -s '$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/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_IMPUTE_VALUES@"><![CDATA[ + #import re + #set $impute_values = {} + #if $abundance_file: + #silent $impute_values['abundances']='min' + #end if + #if $me_or_frac_contrib_file: + #silent $impute_values['mean_enrichment']='min' + #end if + ]]></token> + <token name="@INIT_DATATYPES@"><![CDATA[ + #import re + #set $datatypes_avail = list() + #if str( $data_input.data_input_selector ) == "abundance": + #if $data_input.abundance_file: + $datatypes_avail.append(re.sub('"', '', "abundances")) + #end if + #elif str( $data_input.data_input_selector ) == "mean_enrichment": + #if $data_input.me_or_frac_contrib_file: + $datatypes_avail.append(re.sub('"', '', "mean_enrichment")) + #end if + #elif str( $data_input.data_input_selector ) == "isotop_prop": + #if $data_input.isotop_prop_file: + $datatypes_avail.append(re.sub('"', '', "isotopologue_proportions")) + #end if + #else + #if $data_input.isotop_abs_file: + $datatypes_avail.append(re.sub('"', '', "isotopologues")) + #end if + #end if + ]]></token> + <token name="@INIT_STAT_TEST@"><![CDATA[ + #import re + #set $statistical_test = {} + #if str( $data_input.data_input_selector ) == "abundance": + #if $data_input.abundance_file: + #silent $statistical_test['abundances']=str($data_input.stat_test) + #end if + #elif str( $data_input.data_input_selector ) == "mean_enrichment": + #if $data_input.me_or_frac_contrib_file: + #silent $statistical_test['mean_enrichment']=str($data_input.stat_test) + #end if + #elif str( $data_input.data_input_selector ) == "isotop_prop": + #if $data_input.isotop_prop_file: + #silent $statistical_test['isotopologue_proportions']=str($data_input.stat_test) + #end if + #else + #if $data_input.isotop_abs_file: + #silent $statistical_test['isotopologues']=str($data_input.stat_test) + #end if + #end if + ]]></token> + <token name="@INIT_CONDITIONS@"><![CDATA[ + #import re + #set $conds = list() + #for $co in $conditions: + $conds.append(re.sub('"', '', str($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 + #set $timepoints = list() + #for $tp in $timepoint: + $timepoints.append(re.sub('"', '', str($tp))) + #end for + ]]></token> + <token name="@INIT_GROUPS@"><![CDATA[ + #import re + #set $groups = list() + $groups.append(re.sub('"', '', str("condition"))) + $groups.append(re.sub('"', '', str("timepoint"))) + + ]]></token> + <token name="@INIT_ENRICHMENT_METABOLITES@"><![CDATA[ + #import json + #import re + #set $metabolites = {} + #for $cp in $compartments: + #silent $metabolites[re.sub('"', '', str($cp))]=list() + #for $met in $metabolites_list: + #set tmp_met=re.sub('\,', '%%',str($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> + <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[ + #set $metabolites = {} + #for $cp in $compartments: + #silent $metabolites[re.sub('"', '', str($cp))]=list() + #for $met in $metabolites_list: + #set tmp_met=re.sub('\,', '--',str($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> + <token name="@INIT_MULTIGROUP_COMPARISONS@"><![CDATA[ + #set $comparisons = list() + #for $tp in $timepoint: + #set $ctrl_found=False + #set $ctrl="" + + #for $co in $conditions: + #set $sub_comparisons = list() + #if str($co) in ["Control", "control","ctrl"]: + #set $ctrl_found=True + #set $ctrl=str($co) + $sub_comparisons.append(re.sub('"', '', str($co))) + $sub_comparisons.append(re.sub('"', '', str($tp))) + #else: + $sub_comparisons.append(re.sub('"', '', str($co))) + $sub_comparisons.append(re.sub('"', '', str($tp))) + + #end if + $comparisons.append($sub_comparisons) + #end for + #end for + ]]></token> + <token name="@INIT_CONDITIONS_TIMECOURSE@"><![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 + + ]]></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[ + #import re + #set $conds = list() + #for $co in $conditions: + $conds.append(re.sub('"', '', str($co))) + #end for + #set $timepoints = list() + #for $tp in $timepoint: + $timepoints.append(re.sub('"', '', str($tp))) + #end for + + #set $comparisons = list() + #if len($conds) > 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($conds) > 0: + #if len($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_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 + #import subprocess + #set $transcripts = list() + + #for $i, $s in enumerate($deg_list) + #set $cpt = str($i+1) + $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1))) + #set $deg_one_values = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.valuecol), shell=True)) + #set $deg_one_id = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.idcol), shell=True)) + #end for + ]]></token> + <token name="@INIT_PATHWAYS@"><![CDATA[ + #set $pathways = {} + #if $path_kegg_metabolites: + #silent $pathways['metabolites']='pathways_kegg_metabolites' + #end if + #if $path_kegg_transcripts: + #silent $pathways['transcripts']='pathways_kegg_transcripts' + #end if + ]]></token> +</macros>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CorrectedIsotopologues_5.csv Thu Feb 15 12:53:48 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/CorrectedIsotopologues_reduced.csv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,46 @@ +"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 1 1 1 1 +"Fructose_1,6-bisphosphate_m+1" 0 0 0 0 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 0 0 0 0 +"Fructose_1,6-bisphosphate_m+5" 0 0 0 0 0 +"Fructose_1,6-bisphosphate_m+6" 0 0 0 0 0 +"L-Aspartic_acid_m+0" 0.9863 0.9866 0.745 0.7303 0.982 0.9831 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 0.0004 0.0008 0.0589 0.0596 +"L-Aspartic_acid_m+4" 0 0.0001 0.007 0.012 0.0003 0 0.0117 0.0143 +"L-Glutamic_acid_m+0" 0.9491 0.9486 0.5577 0.5714 0.9508 0.9458 0.5577 0.5556 +"L-Glutamic_acid_m+1" 0.0103 0.0095 0.0737 0.0687 0.0084 0.0109 0.0715 0.0688 +"L-Glutamic_acid_m+2" 0.0399 0.0409 0.2485 0.2455 0.0387 0.0408 0.2477 0.2507 +"L-Glutamic_acid_m+3" 0 0.0004 0.0619 0.057 0.0006 0.001 0.0628 0.0625 +"L-Glutamic_acid_m+4" 0.0008 0.0006 0.0487 0.0477 0.0015 0.0015 0.0508 0.0506 +"L-Glutamic_acid_m+5" 0 0 0.0094 0.0096 0 0 0.0095 0.0118 +"L-Glutamine_m+0" 1 1 0.7483 0.7005 0.997 0.9986 0.7153 0.6673 +"L-Glutamine_m+1" 0 0 0.0347 0.0402 0 0 0.0424 0.0526 +"L-Glutamine_m+2" 0.01 0.0104 0.1482 0.1693 0.009 0.0104 0.1757 0.1919 +"L-Glutamine_m+3" 0 0 0.0371 0.049 0 0 0.0363 0.043 +"L-Glutamine_m+4" 0 0 0.0263 0.0341 0 0 0.0268 0.0374 +"L-Glutamine_m+5" 0 0 0.0053 0.007 0 0 0.0034 0.0078 +"L-Lactic_acid_m+0" 0 0 0 0 0 0 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 0 0 0 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 0.0122 0.0117 0.012 0.012 0.0116 0.0113 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 0.9878 0.9883 0.988 0.988 0.9884 0.9887 0.9723 0.9709 0.9704 0.9687 0.9731 0.9742 0.9651 0.9713 +"L-Lysine_m+0" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +"L-Lysine_m+1" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Lysine_m+2" 0.0015 0.0004 0.0006 0.001 0.0006 0.0009 0.0018 0.0008 0 0 0 0 0 0 0 0 +"L-Lysine_m+3" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Lysine_m+4" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Lysine_m+5" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Lysine_m+6" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Proline_m+0" 0.9717 0.9719 0.9461 0.95 0.9813 0.9779 0.9602 0.9617 0.9939 0.9872 0.9545 1 1 1 0.9869 1 +"L-Proline_m+1" 0.0296 0.0306 0.0279 0.0284 0.0208 0.0244 0.0167 0.0061 0.0076 0.0147 0.0488 0 0 0 0.0149 0.0013 +"L-Proline_m+2" 0 0 0.0248 0.0213 0 0 0.0214 0.0302 0 0 0 0 0 0 0 0 +"L-Proline_m+3" 0 0 0 0 0 0 0 0.001 0 0 0.0001 0 0 0 0 0 +"L-Proline_m+4" 0 0 0.0021 0.0011 0 0 0.0025 0.0009 0 0 0 0 0 0 0 0 +"L-Proline_m+5" 0.0012 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Serine_m+0" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +"L-Serine_m+1" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Serine_m+2" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Serine_m+3" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell--multigroup.tsv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,6 @@ +metabolite Ctrl_cell_T0h-1 Ctrl_cell_T0h-2 Ctrl_cell_T0h-3 Cond1_cell_T0h-1 Cond1_cell_T0h-2 Cond1_cell_T0h-3 Cond2_cell_T0h-1 Cond2_cell_T0h-2 Cond2_cell_T0h-3 Ctrl_cell_T2h-1 Ctrl_cell_T2h-2 Ctrl_cell_T2h-3 Cond1_cell_T2h-1 Cond1_cell_T2h-2 Cond1_cell_T2h-3 Cond2_cell_T2h-1 Cond2_cell_T2h-2 Cond2_cell_T2h-3 pvalue padj +Glycine 0.002519 0.003212 0.002011 0.009304 0.010108 0.014663 2.87541 1.698859 1.731678 0.00015 0.000175 9.8e-05 4.5e-05 1.579707 5.3e-05 1.787379 2.109744 2.1255 0.018127 0.090635 +Hexose 0.001174 0.00082 0.001356 0.000516 0.000519 0.000437 1.843131 1.834915 2.0687 0.000169 0.000253 0.000164 1.865063 1.718398 1.76228 1.987815 2.449479 2.241466 0.006794 0.033971 +L-Arginine 0.000151 0.000198 0.000111 7.8e-05 0.00012 2.038458 2.026891 2.02749 1.983931 0.000108 0.000137 9.9e-05 2.034691 1.974143 1.917751 1.991686 0.167953 0.839766 +L-Glutamine 1.58483 1.81629 1.751614 0.754035 0.894641 3.490867 3.443824 2.831176 +L-Tryptophan 6.3e-05 7.3e-05 7e-05 0.000491 0.000499 4.483307 0.344618 0.318892 0.313476 4e-05 4.5e-05 3.2e-05 0.369116 0.35728 0.292317 0.331011 0.300477 0.331022 0.030637 0.153184
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-Control-L-Cycloserine-pearson.tsv Thu Feb 15 12:53:48 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--cell-Control-T0-L-Cycloserine-T0-Tt.tsv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,25 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_cell_T0-1 Ctrl_cell_T0-2 L-Cyc_cell_T0-1 L-Cyc_cell_T0-2 gmean_1 gmean_2 +L-Tyrosine 0.659969 0.044578 1.0 0.544 1.580048 0 0 1.346502 2.475187 cell 5.059224 5.449813 3.712722 2.974626 5.250888 3.323245 +L-Methionine 0.564183 0.075348 1.0 0.488153 1.47855 0 0 1.21324 2.485367 cell 5.928871 5.711734 4.498494 3.443504 5.81929 3.935808 +L-Aspartic_acid 1.159351 0.071437 1.0 0.435311 2.23357 0 0 1.126485 2.587769 cell 3.824739 2.962785 1.8363 1.23697 3.366286 1.507132 +Ile_Leu 0.693524 0.078103 1.0 0.414254 1.617229 0 0 1.080144 2.607445 cell 4.393714 5.288745 3.31357 2.6813 4.820501 2.980717 +L-Tryptophan 0.837035 0.077877 1.0 0.411565 1.786375 0 0 1.07544 2.613053 cell 3.918551 4.59966 2.843111 1.986607 4.245468 2.376582 +L-Phenylalanine 0.676734 0.082439 1.0 0.397203 1.598517 0 0 1.043392 2.62685 cell 4.492276 5.358136 3.448884 2.731286 4.906142 3.069184 +L-Histidine 0.662413 0.124722 1.0 0.342512 1.582728 0 0 0.893231 2.607882 cell 5.135867 4.726362 3.833131 2.527985 4.926862 3.112892 +L-Lysine 0.700054 0.108484 1.0 0.32716 1.624566 0 0 0.879075 2.68699 cell 4.289814 5.133306 3.410739 2.446316 4.692646 2.888554 +L-Valine 0.48785 0.113542 1.0 0.317079 1.402354 0 0 0.853637 2.692194 cell 6.655174 5.844043 4.990406 3.96298 6.236435 4.44712 +L-Glutamic_acid 0.830004 0.137338 1.0 0.265185 1.777691 0 0 0.723262 2.727386 cell 4.556485 3.416118 2.692856 1.829099 3.945312 2.219347 +L-Serine 0.556596 0.152386 1.0 0.23191 1.470794 0 0 0.638261 2.752194 cell 5.905558 4.753595 4.115334 3.153364 5.298361 3.602381 +Hexose-phosphate 0.76747 0.157597 1.0 0.22649 1.702282 0 0 0.62225 2.747362 cell 4.735898 3.493336 2.871086 1.988536 4.067442 2.389405 +L-Proline 0.519615 0.177905 1.0 0.223644 1.433572 0 0 0.601013 2.687365 cell 6.102914 4.603201 4.002188 3.415549 5.300277 3.697252 +L-Lactic_acid 0.766316 0.216319 1.0 0.194497 1.70092 0 0 0.51042 2.624306 cell 2.828561 4.538379 2.318141 1.914073 3.582887 2.10644 +Hexose 0.648059 0.202852 1.0 0.1683 1.567058 0 0 0.459334 2.729259 cell 5.122919 3.575551 3.116217 2.39366 4.279867 2.731147 +Fumaric_acid 0.623283 0.19388 1.0 0.156841 1.540376 0 0 0.437164 2.787315 cell 3.977834 5.293909 2.506594 3.54067 4.588931 2.979098 +L-Malic_acid 0.276766 0.295582 1.0 0.151833 1.211476 0 0 0.371422 2.446251 cell 8.445961 8.514381 8.074539 6.06813 8.480102 6.999811 +L-Arginine 0.574794 0.200943 1.0 0.144438 1.489464 0 0 0.403393 2.792837 cell 4.234461 5.565819 3.831068 2.772982 4.854714 3.259368 +L-Threonine 0.540842 0.220629 1.0 0.113082 1.454821 0 0 0.316715 2.800767 cell 5.715582 4.30713 3.990415 2.914815 4.961628 3.410472 +L-Glutamine 0.98619 0.263749 1.0 0.087801 1.980946 0 0 0.237703 2.707301 cell 3.806965 2.018081 1.780378 1.099664 2.77178 1.39922 +Glycine 0.567169 0.318145 1.0 -0.012773 1.481613 0 0 -0.035287 2.762706 cell 5.028385 3.20148 3.236767 2.265679 4.012265 2.708039 +Pyruvic_acid 0.472738 0.490805 1.0 -0.131405 1.387741 0 0 -0.317152 2.413541 cell 1.811325 4.224866 2.158282 1.84113 2.766334 1.993409 +L-Alanine 0.440859 0.494601 1.0 -0.237912 1.357412 0 0 -0.631111 2.652708 cell 4.684396 2.511054 3.142165 2.031688 3.42969 2.526638 +Fructose_1,6-bisphosphate 2.638184 1 1 2.0 cell 3.220864 1.220864 3.220864 1.220864
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-Control-T2h-Control-T0-Tt.tsv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,25 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_cell_T2h-1 Ctrl_cell_T2h-2 Ctrl_cell_T0-1 Ctrl_cell_T0-2 gmean_1 gmean_2 +L-Tryptophan -0.777998 0.034692 0.69385 0.664552 0.583176 0 0 1.541549 2.319681 cell 2.660282 2.70099 4.242539 4.979963 2.680559 4.596486 +L-Aspartic_acid -2.274085 0.039066 0.781312 0.556683 0.206744 0 0 1.374553 2.469185 cell 0.327076 0.791534 2.796261 2.166087 0.508814 2.461086 +L-Lysine -0.558396 0.071556 1.0 0.497716 0.679057 0 0 1.23415 2.479625 cell 3.776027 3.993588 5.227738 6.255652 3.883284 5.718646 +L-Arginine -0.658636 0.111701 1.0 0.440969 0.633477 0 0 1.087359 2.465839 cell 3.035924 2.953846 4.123283 5.419685 2.994604 4.72725 +L-Histidine -0.68301 0.090057 1.0 0.413676 0.622865 0 0 1.065086 2.574685 cell 2.578187 3.676926 5.152872 4.742012 3.078929 4.943175 +L-Tyrosine -0.589456 0.191484 1.0 0.235832 0.664593 0 0 0.617152 2.616914 cell 2.671781 4.292502 4.909654 5.288695 3.386536 5.095651 +L-Methionine -0.489868 0.261207 1.0 0.168943 0.71209 0 0 0.427099 2.528072 cell 3.0957 4.99071 5.623772 5.417809 3.930616 5.51983 +L-Phenylalanine -0.608451 0.19931 1.0 0.160334 0.655901 0 0 0.442554 2.760207 cell 2.526754 3.990049 4.432603 5.286961 3.175196 4.840971 +L-Malic_acid -0.842519 0.323037 1.0 0.123892 0.557669 0 0 0.2985 2.409353 cell 1.235551 3.317115 3.615615 3.644904 2.024467 3.63023 +Ile_Leu -0.554218 0.227774 1.0 0.111354 0.681026 0 0 0.309498 2.779406 cell 2.749607 4.283823 4.593321 5.529013 3.43203 5.039497 +L-Lactic_acid -0.468969 0.32893 1.0 0.109159 0.722481 0 0 0.264176 2.420103 cell 3.143658 3.203459 3.467635 5.563761 3.173418 4.39239 +Fumaric_acid -1.082458 0.257085 1.0 0.072691 0.472224 0 0 0.201376 2.770286 cell 0.878066 2.539989 2.741365 3.648352 1.493412 3.162509 +L-Glutamine -1.091499 0.265783 1.0 0.064303 0.469274 0 0 0.177439 2.759429 cell 0.883383 1.753625 3.642812 1.931064 1.244638 2.652264 +L-Glutamic_acid -0.765842 0.325511 1.0 -0.028187 0.58811 0 0 -0.078254 2.776208 cell 1.414087 3.21983 4.190295 3.141576 2.133804 3.628241 +L-Valine -0.345997 0.35338 1.0 -0.044413 0.786764 0 0 -0.120212 2.706693 cell 4.179372 6.167004 6.886065 6.046792 5.07683 6.452798 +L-Threonine -0.463814 0.368868 1.0 -0.099423 0.725067 0 0 -0.278707 2.803234 cell 2.723045 4.443183 5.526279 4.164476 3.47836 4.797297 +Pyruvic_acid 0.905946 0.398774 1.0 -0.124124 1.873772 0 0 -0.34081 2.745715 cell 1.633721 3.592255 0.84654 1.974531 2.422549 1.292873 +Hexose-phosphate -0.60704 0.407318 1.0 -0.137592 0.656542 0 0 -0.378236 2.748963 cell 1.734049 3.685036 4.483012 3.3068 2.527851 3.85025 +Hexose -0.403635 0.446592 1.0 -0.201612 0.755951 0 0 -0.558993 2.772623 cell 2.764282 4.423486 5.536905 3.864493 3.496822 4.625725 +L-Serine -0.31232 0.458611 1.0 -0.2056 0.805345 0 0 -0.560471 2.726026 cell 3.868814 5.868893 6.59484 5.308422 4.765045 5.916772 +Fructose_1,6-bisphosphate 0.0 1.526778 0 1 0.0 2.23249 cell 0.154691 2.387181 0.398015 0.60768 0.398015 +Glycine -0.316365 0.624652 -0.423447 0.803091 0 0 -1.102692 2.604084 cell 2.393939 4.284841 4.998023 3.182149 3.202756 3.988039 +L-Proline -0.168249 0.862102 -0.454948 0.889922 0 0 -1.160081 2.549919 cell 2.590021 5.13994 4.720818 3.560737 3.648637 4.09995 +L-Alanine -0.07162 0.950212 -0.89366 0.951569 0 0 -1.882381 2.106373 cell 1.96331 4.069683 4.057263 2.174882 2.826668 2.970533
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,25 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_cell_T2h-1 Ctrl_cell_T2h-2 L-Cyc_cell_T2h-1 L-Cyc_cell_T2h-2 gmean_1 gmean_2 +L-Lactic_acid 0.362066 0.35792 1.0 0.058568 1.285265 0 0 0.142099 2.42622 cell 6.256224 6.375234 3.949014 6.114125 6.315449 4.913732 +L-Arginine 0.181307 0.654333 1.0 -0.072802 1.133911 0 0 -0.192713 2.64707 cell 7.128152 6.935439 5.016926 7.663996 7.031135 6.200782 +L-Tryptophan 0.10835 0.575344 1.0 -0.075459 1.077995 0 0 -0.192682 2.553471 cell 12.591879 12.784561 10.562173 13.115644 12.687854 11.769864 +L-Lysine 0.11389 0.744288 1.0 -0.171533 1.082142 0 0 -0.462286 2.695029 cell 8.023523 8.485809 6.395727 9.090756 8.251429 7.62509 +Fumaric_acid 0.29413 0.461999 0 1 0.700935 2.383081 cell 0.888751 2.570897 3.271832 1.511584 3.271832 +Fructose_1,6-bisphosphate 0.0 1.145529 0 1 0.0 2.287469 cell 0.158501 2.44597 0.543545 0.622647 0.543545 +Pyruvic_acid 0.373873 0.661572 -0.465941 1.295827 0 0 -1.181049 2.534762 cell 1.800099 3.958089 1.423327 2.981148 2.669261 2.05989 +L-Glutamine 0.262582 0.678179 -0.482549 1.199624 0 0 -1.200459 2.487743 cell 2.308578 4.582813 2.09507 3.509037 3.252658 2.711398 +L-Aspartic_acid 0.249699 0.745614 -0.577117 1.188959 0 0 -1.388665 2.406211 cell 1.600511 3.873288 1.467077 2.989176 2.489827 2.094123 +Ile_Leu 0.191338 0.775003 -0.624008 1.141823 0 0 -1.493647 2.393636 cell 3.231426 5.034484 2.640848 4.725073 4.033431 3.53245 +L-Phenylalanine 0.185719 0.785147 -0.638734 1.137383 0 0 -1.519477 2.378888 cell 3.147058 4.969585 2.590697 4.666535 3.95469 3.477007 +L-Tyrosine 0.169586 0.805815 -0.669127 1.124736 0 0 -1.570811 2.347552 cell 3.058614 4.91399 2.566438 4.629425 3.876854 3.446902 +L-Valine 0.154185 0.813025 -0.678125 1.112793 0 0 -1.575671 2.32357 cell 3.58809 5.294519 2.970949 5.163761 4.358579 3.916793 +L-Alanine -0.026254 0.973518 -0.688817 0.981966 0 0 -1.603905 2.328493 cell 2.170343 4.498836 2.479673 4.083578 3.124743 3.182128 +L-Histidine 0.111173 0.829889 -0.704841 1.080106 0 0 -1.624902 2.305344 cell 4.258872 6.073864 3.76852 5.883774 5.086041 4.708834 +L-Malic_acid -0.25568 0.834034 -0.711875 0.837592 0 0 -1.640219 2.304084 cell 1.183028 3.176104 1.535885 3.487112 1.938407 2.314261 +Hexose 0.123989 0.851213 -0.738234 1.089743 0 0 -1.678448 2.273598 cell 3.154886 5.048543 2.774945 4.833334 3.990937 3.662272 +Hexose-phosphate 0.02248 0.937522 -0.772684 1.015704 0 0 -1.725995 2.233767 cell 1.985384 4.219151 2.114313 3.840308 2.894242 2.849493 +L-Glutamic_acid 0.071406 0.898587 -0.786571 1.05074 0 0 -1.739625 2.211657 cell 1.73196 3.943617 1.76515 3.504775 2.613463 2.487258 +L-Proline -0.102609 0.921051 -0.798521 0.931347 0 0 -1.759402 2.203325 cell 2.237976 4.441301 2.617836 4.377238 3.152701 3.385098 +L-Threonine 0.069145 0.906001 -0.827452 1.049095 0 0 -1.803085 2.179081 cell 3.176783 5.183546 3.004465 4.979868 4.057955 3.868054 +L-Serine 0.075222 0.909283 -0.832574 1.053523 0 0 -1.804475 2.167344 cell 3.54649 5.379935 3.212591 5.350965 4.368053 4.146138 +L-Methionine 0.080167 0.913957 -0.840739 1.05714 0 0 -1.816896 2.16107 cell 3.053635 4.922895 2.761825 4.870531 3.877206 3.667636 +Glycine -0.003109 0.981504 -0.842581 0.997848 0 0 -1.822182 2.162619 cell 2.737938 4.900557 2.871164 4.693346 3.66298 3.670881
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,25 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment L-Cyc_cell_T2h-1 L-Cyc_cell_T2h-2 L-Cyc_cell_T0-1 L-Cyc_cell_T0-2 gmean_1 gmean_2 +L-Aspartic_acid -1.364433 0.130746 0.522986 0.281466 0.388387 0 0 0.763705 2.713309 cell 0.780152 1.589563 3.493461 2.353268 1.113598 2.867237 +Pyruvic_acid 1.004811 0.273062 1.0 0.153419 2.006681 0 0 0.386767 2.520986 cell 1.764929 3.696632 1.378162 1.175646 2.55427 1.272883 +L-Proline 0.453975 0.375728 1.0 -0.027312 1.36981 0 0 -0.070115 2.567204 cell 3.208945 5.365621 3.27906 2.798417 4.149456 3.029221 +L-Alanine 0.395494 0.490938 1.0 -0.247303 1.315393 0 0 -0.66902 2.705267 cell 3.137119 5.166273 3.806139 2.461006 4.025818 3.060544 +L-Glutamine -0.367891 0.54526 -0.322082 0.774915 0 0 -0.864197 2.683155 cell 2.384944 3.994548 5.068099 3.130351 3.086547 3.98308 +L-Arginine -0.26515 0.569639 -0.353864 0.832112 0 0 -0.942768 2.66421 cell 3.571926 5.456573 6.236136 4.513805 4.414802 5.305535 +Ile_Leu -0.052032 0.999845 -0.372715 0.964577 0 0 -0.987815 2.650324 cell 3.358135 6.008459 5.176894 4.189079 4.491906 4.656868 +Glycine 0.253911 0.601429 -0.381709 1.192436 0 0 -0.98425 2.578534 cell 3.495889 5.714551 4.480139 3.136017 4.469613 3.748305 +L-Tyrosine -0.099074 0.925868 -0.397473 0.933632 0 0 -1.041848 2.621181 cell 3.260853 5.882034 5.240632 4.198784 4.379549 4.690872 +L-Valine -0.012332 0.946093 -0.416211 0.991489 0 0 -1.085262 2.607482 cell 3.532767 6.140249 5.271324 4.186062 4.657475 4.697456 +L-Malic_acid -0.310073 0.749772 -0.421482 0.806601 0 0 -1.063593 2.523462 cell 1.986311 4.509773 4.280295 3.216702 2.99296 3.710584 +L-Phenylalanine -0.117435 0.894656 -0.424837 0.921825 0 0 -1.0998 2.588757 cell 3.230833 5.81959 5.2858 4.186 4.336142 4.703866 +Hexose 0.120435 0.752117 -0.433008 1.087063 0 0 -1.088815 2.51454 cell 3.389891 5.904431 4.695803 3.606988 4.473855 4.115544 +L-Lactic_acid -0.064719 0.922245 -0.455322 0.956131 0 0 -1.16852 2.566358 cell 4.680861 7.247219 6.703809 5.535289 5.824365 6.091594 +L-Serine 0.169053 0.680458 -0.460513 1.12432 0 0 -1.121076 2.434406 cell 3.657336 6.091742 4.795994 3.674918 4.720122 4.1982 +L-Methionine -0.005852 0.938944 -0.468109 0.995952 0 0 -1.196896 2.556876 cell 3.348806 5.905682 5.10358 3.906684 4.447132 4.465207 +Hexose-phosphate 0.13795 0.760717 -0.55418 1.10034 0 0 -1.331177 2.402066 cell 2.942487 5.344553 4.330543 2.999366 3.965637 3.604009 +L-Glutamic_acid -0.007244 0.937477 -0.559258 0.994991 0 0 -1.377884 2.46377 cell 2.49992 4.96369 4.295701 2.917817 3.522617 3.540349 +L-Tryptophan -0.049313 0.852261 -0.581752 0.966396 0 0 -1.40667 2.417988 cell 5.818548 7.225218 8.026356 5.608368 6.483847 6.709304 +L-Threonine 0.007882 0.940534 -0.614186 1.005478 0 0 -1.477656 2.405876 cell 3.659188 6.065064 5.482022 4.004366 4.710967 4.685299 +L-Histidine -0.131769 0.796273 -0.655487 0.912712 0 0 -1.55048 2.365386 cell 3.449234 5.385275 5.81462 3.834795 4.309881 4.722063 +L-Lysine 0.027768 0.93853 -0.883894 1.019434 0 0 -1.871833 2.117711 cell 4.914168 6.984898 6.786001 4.867187 5.858751 5.747063 +Fructose_1,6-bisphosphate 3.516217 1 1 2.0 cell 2.794844 0.794844 2.794844 0.794844 +Fumaric_acid 1.574466 1 0 1.289051 cell 5.258464 2.81012 3.969413 5.258464 3.339839
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-Control-L-Cycloserine-pearson.tsv Thu Feb 15 12:53:48 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/abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,20 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_med_T0-1 Ctrl_med_T0-2 L-Cyc_med_T0-1 L-Cyc_med_T0-2 gmean_1 gmean_2 +L-Valine -0.06551 0.004613 0.078425 0.830536 0.955607 0 0 1.806475 2.175072 med 42.7862 42.917067 44.961272 44.723542 42.851584 44.842249 +L-Lactic_acid 0.081287 0.035485 0.603247 0.64986 1.057961 0 0 1.519643 2.338416 med 35.285733 35.209883 33.69024 32.947317 35.247788 33.316708 +L-Arginine 0.006662 0.038909 0.661461 0.622566 1.004628 0 0 1.475052 2.369309 med 417.573697 416.802075 415.204388 415.327023 417.187708 415.265701 +L-Proline -0.114311 0.052379 0.890451 0.495962 0.923823 0 0 1.256673 2.533809 med 22.674872 23.296347 25.208681 24.55302 22.983509 24.878691 +Hexose-phosphate -0.152217 0.121088 1.0 0.441254 0.899867 0 0 1.07635 2.439298 med 15.686678 15.672772 18.11207 16.763028 15.679723 17.424498 +L-Tryptophan 0.139342 0.13131 1.0 0.32956 1.101403 0 0 0.861293 2.613467 med 18.793992 19.207497 17.932699 16.59403 18.99962 17.250384 +L-Phenylalanine -0.070754 0.112054 1.0 0.327323 0.95214 0 0 0.875883 2.675902 med 34.932908 35.642687 37.60881 36.51857 35.286013 37.059681 +L-Methionine -0.05948 0.121063 1.0 0.296729 0.95961 0 0 0.804505 2.711241 med 41.3005 42.222702 44.011741 43.027207 41.759055 43.51669 +L-Alanine -0.186768 0.189622 1.0 0.161521 0.878572 0 0 0.450765 2.790747 med 11.17805 12.28269 13.968797 12.733455 11.71736 13.336831 +Ile_Leu -0.067879 0.266664 1.0 0.038434 0.95404 0 0 0.108567 2.824776 med 29.783216 31.074798 32.607992 31.183365 30.422153 31.887724 +Glycine -0.40224 0.406096 1.0 0.003298 0.756683 0 0 0.00781 2.367806 med 3.275612 3.189559 5.557365 3.283422 3.232299 4.271671 +Pyruvic_acid -0.059155 0.334667 1.0 0.001586 0.959826 0 0 0.004213 2.65712 med 33.153112 31.141204 33.798324 33.157325 32.131415 33.47629 +L-Lysine -0.001834 0.946483 1.0 -0.206473 0.99873 0 0 -0.57111 2.766029 med 90.619429 93.385458 92.395033 91.823923 91.992048 92.109035 +L-Threonine -0.019183 0.467268 1.0 -0.208828 0.986792 0 0 -0.562452 2.693379 med 81.007696 78.916447 81.609826 80.445244 79.955235 81.025443 +L-Asparagine 0.051495 0.479539 1.0 -0.240516 1.036338 0 0 -0.659285 2.74113 med 30.611703 29.072045 29.73133 27.870573 29.831943 28.78592 +Hexose 0.007394 0.632326 1.0 -0.248644 1.005138 0 0 -0.634685 2.552587 med 141.526046 144.078633 142.384333 141.749648 142.796636 142.066636 +L-Serine -0.003785 0.885659 1.0 -0.258807 0.99738 0 0 -0.70402 2.720251 med 82.756733 83.460753 84.697551 81.9773 83.107998 83.326326 +L-Histidine 0.020108 0.536681 -0.307902 1.014035 0 0 -0.82449 2.677766 med 66.478417 67.955877 65.278111 67.302907 67.213087 66.282778 +L-Tyrosine -0.024305 0.567197 -0.345223 0.983294 0 0 -0.912759 2.643971 med 49.917227 51.3987 52.561198 50.485941 50.652548 51.51312
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-Control-T2h-Control-T0-Tt.tsv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,20 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_med_T2h-1 Ctrl_med_T2h-2 Ctrl_med_T0-1 Ctrl_med_T0-2 gmean_1 gmean_2 +L-Asparagine -0.315743 0.028245 0.508416 0.610328 0.803437 0 0 1.473213 2.413806 med 7.730141 8.16053 10.143947 9.633743 7.942421 9.885554 +L-Phenylalanine -0.084598 0.030111 0.541993 0.671736 0.943047 0 0 1.558881 2.320675 med 32.130034 32.052743 33.688915 34.373418 32.091365 34.029445 +L-Threonine -0.106792 0.033603 0.604856 0.631099 0.928651 0 0 1.495659 2.369928 med 25.045012 25.211552 27.41494 26.707211 25.128144 27.058762 +L-Valine -0.067996 0.042832 0.770972 0.607069 0.953962 0 0 1.446278 2.382394 med 39.306545 40.115539 41.561817 41.688939 39.708982 41.625329 +L-Tyrosine -0.113457 0.046722 0.840993 0.530543 0.924371 0 0 1.321767 2.491346 med 23.066568 23.499488 24.821255 25.557914 23.282022 25.186891 +L-Serine -0.118888 0.05061 0.910985 0.560837 0.920897 0 0 1.364531 2.433027 med 22.588437 21.723711 23.952968 24.156738 22.151855 24.054637 +Hexose-phosphate -0.427357 0.062717 1.0 0.581387 0.743623 0 0 1.378344 2.370787 med 5.030212 6.016094 7.400999 7.394438 5.501112 7.397718 +L-Arginine -0.065823 0.085013 1.0 0.501611 0.9554 0 0 1.222599 2.437347 med 39.86267 38.723983 41.16133 41.085269 39.289202 41.123282 +Hexose -0.087076 0.058805 1.0 0.475511 0.941429 0 0 1.21327 2.551509 med 29.894783 30.658183 31.871453 32.446292 30.274077 32.157588 +L-Histidine -0.096367 0.062761 1.0 0.459013 0.935385 0 0 1.179441 2.569515 med 27.526594 26.774502 28.706035 29.344017 27.147944 29.023273 +Glycine -0.100796 0.063723 1.0 0.454918 0.932518 0 0 1.171006 2.574101 med 26.206344 25.541879 28.11598 27.37735 25.871978 27.744207 +Ile_Leu -0.087322 0.110833 1.0 0.415844 0.941268 0 0 1.04462 2.512048 med 28.487629 28.300899 29.532249 30.812947 28.39411 30.165802 +L-Proline -0.427205 0.130273 1.0 0.377685 0.743701 0 0 0.953724 2.525185 med 5.916471 4.533309 6.870195 7.058494 5.178918 6.963708 +L-Methionine -0.104127 0.121198 1.0 0.325756 0.930368 0 0 0.863734 2.651476 med 22.963857 24.192125 25.055859 25.615333 23.569991 25.334052 +L-Lysine -0.042176 0.194447 1.0 0.300247 0.971189 0 0 0.744058 2.478156 med 54.067768 54.127004 54.871062 56.545924 54.097378 55.702198 +L-Lactic_acid -0.056578 0.275137 1.0 0.176712 0.961542 0 0 0.435423 2.464029 med 37.556173 35.609409 38.073438 37.991596 36.569839 38.032495 +L-Tryptophan -0.176081 0.342876 1.0 0.050641 0.885104 0 0 0.126694 2.501802 med 11.638726 9.52248 11.76542 12.024282 10.527561 11.894147 +L-Alanine -0.072231 0.842985 1.0 -0.299141 0.951166 0 0 -0.800552 2.67617 med 6.849088 9.525258 8.100928 8.90148 8.077087 8.491775 +Pyruvic_acid 0.004852 0.940585 -0.575253 1.003369 0 0 -1.407863 2.447382 med 39.928124 38.520261 40.329053 37.881671 39.217875 39.086211
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-Control-T2h-L-Cycloserine-T2h-Tt.tsv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,20 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_med_T2h-1 Ctrl_med_T2h-2 L-Cyc_med_T2h-1 L-Cyc_med_T2h-2 gmean_1 gmean_2 +L-Phenylalanine -0.227241 0.001876 0.035636 0.905036 0.854267 0 0 1.896738 2.09576 med 11.714351 11.686171 13.781931 13.611089 11.700253 13.696244 +L-Tyrosine -0.210967 0.004909 0.093265 0.822767 0.863958 0 0 1.796671 2.183694 med 12.524246 12.759305 14.555976 14.70794 12.641229 14.631761 +Ile_Leu -0.219893 0.005939 0.112833 0.826897 0.858629 0 0 1.799743 2.176503 med 12.110445 12.031063 14.207566 13.910188 12.070689 14.058091 +L-Valine -0.160198 0.012825 0.24368 0.722278 0.894902 0 0 1.65598 2.292719 med 16.643609 16.986162 18.642142 18.936328 16.814013 18.788659 +L-Threonine -0.159992 0.019541 0.371286 0.7134 0.89503 0 0 1.632915 2.28892 med 16.648332 16.759038 18.937252 18.391953 16.703593 18.662611 +L-Proline -0.98264 0.022874 0.434602 0.658092 0.506053 0 0 1.551275 2.35723 med 2.305637 1.766621 3.856912 4.123851 2.018214 3.988149 +Hexose -0.2207 0.024599 0.467389 0.64383 0.858149 0 0 1.52812 2.373482 med 11.643072 11.940391 14.016554 13.468511 11.790794 13.7398 +Glycine -0.173877 0.028221 0.536206 0.613466 0.886457 0 0 1.477944 2.409171 med 15.362891 14.973364 16.840835 17.382535 15.166877 17.109541 +L-Serine -0.217541 0.030833 0.585825 0.595079 0.86003 0 0 1.446276 2.430393 med 12.143564 11.678687 13.58984 14.10908 11.908857 13.847026 +L-Histidine -0.137109 0.034656 0.658468 0.574503 0.909339 0 0 1.408935 2.45244 med 19.638732 19.102155 21.047667 21.554595 19.368585 21.299623 +L-Methionine -0.207039 0.045452 0.863579 0.525451 0.866313 0 0 1.3152 2.502993 med 12.063407 12.708642 14.023842 14.5664 12.381822 14.292547 +L-Lysine -0.025559 0.104493 1.0 0.448561 0.98244 0 0 1.10921 2.472817 med 100.041785 100.151388 102.514602 101.260598 100.096571 101.885671 +Hexose-phosphate -0.359685 0.092784 1.0 0.440559 0.779335 0 0 1.109796 2.519066 med 5.940748 7.105089 8.214885 8.459814 6.496887 8.33645 +L-Asparagine -0.341921 0.124809 1.0 0.353378 0.78899 0 0 0.914077 2.586687 med 6.281405 6.631133 7.54521 8.868092 6.453901 8.179952 +L-Lactic_acid -0.10481 0.179465 1.0 0.178872 0.929927 0 0 0.498003 2.784136 med 22.37888 21.218847 22.876883 24.002983 21.791146 23.43317 +L-Arginine -0.030855 0.279162 1.0 0.132376 0.97884 0 0 0.337068 2.546283 med 67.988605 66.046493 68.325673 68.592776 67.010514 68.459094 +L-Alanine -0.443451 0.222838 1.0 0.113513 0.735373 0 0 0.3169 2.79175 med 3.755311 5.222638 5.539538 6.547061 4.428615 6.022266 +Pyruvic_acid -0.070842 0.413764 1.0 -0.116088 0.952082 0 0 -0.307971 2.652915 med 23.31152 22.489558 23.003549 25.142473 22.896851 24.049243 +L-Tryptophan 0.004678 0.946377 1.0 -0.26993 1.003247 0 0 -0.736036 2.726765 med 14.996403 12.269638 13.157757 13.893793 13.564676 13.520767
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,20 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment L-Cyc_med_T2h-1 L-Cyc_med_T2h-2 L-Cyc_med_T0-1 L-Cyc_med_T0-2 gmean_1 gmean_2 +L-Arginine -0.028306 0.009613 0.163421 0.808209 0.980571 0 0 1.770679 2.190869 med 99.783635 100.173715 101.944394 101.974504 99.978485 101.959448 +L-Proline 0.441124 0.016987 0.288782 0.718846 1.357661 0 0 1.64444 2.287611 med 7.203777 7.702354 5.559337 5.414743 7.448895 5.486564 +Hexose 0.141018 0.04318 0.734054 0.618875 1.102683 0 0 1.46312 2.364161 med 20.919801 20.101843 18.638723 18.55564 20.506744 18.597135 +Hexose-phosphate -0.21989 0.073263 1.0 0.469101 0.858631 0 0 1.183673 2.523277 med 11.042011 11.371231 13.565288 12.554904 11.205412 13.050321 +L-Lactic_acid 0.129519 0.080906 1.0 0.431162 1.093929 0 0 1.107572 2.568806 med 20.843746 21.869766 19.736174 19.30096 21.350594 19.517354 +L-Phenylalanine 0.071888 0.086895 1.0 0.411507 1.051091 0 0 1.064817 2.587604 med 37.870329 37.400886 36.336069 35.282725 37.634876 35.805524 +L-Tyrosine 0.073205 0.130892 1.0 0.338927 1.052051 0 0 0.880001 2.596432 med 35.077787 35.443998 34.197786 32.847566 35.260417 33.515877 +L-Serine 0.094869 0.119025 1.0 0.303502 1.067968 0 0 0.820491 2.703409 med 27.149162 28.186476 26.328671 25.483067 27.662957 25.902419 +L-Valine 0.026692 0.156019 1.0 0.275356 1.018673 0 0 0.72888 2.647043 med 91.228609 92.66826 90.499729 90.021217 91.945617 90.260156 +L-Histidine 0.06085 0.160307 1.0 0.217054 1.04308 0 0 0.599017 2.759755 med 40.2211 41.189815 38.43006 39.622083 40.702576 39.02152 +L-Lysine -0.018451 0.203814 1.0 0.160847 0.987293 0 0 0.441277 2.743465 med 124.61713 123.092758 125.836223 125.058407 123.852599 125.446712 +Ile_Leu 0.064692 0.208392 1.0 0.155183 1.045861 0 0 0.425368 2.741066 med 36.641515 35.874575 35.449207 33.900449 36.256017 34.66618 +L-Threonine 0.034018 0.28585 1.0 0.039028 1.02386 0 0 0.107299 2.749299 med 61.975824 60.191229 60.08393 59.226525 61.077009 59.653687 +L-Methionine 0.043433 0.307379 1.0 -0.00305 1.030563 0 0 -0.008477 2.778959 med 45.649117 47.415202 45.657594 44.636243 46.52378 45.14403 +L-Alanine 0.184452 0.318436 1.0 -0.007446 1.136385 0 0 -0.020451 2.746709 med 10.230133 12.090774 10.250584 9.344065 11.121611 9.786834 +Glycine -0.329159 0.464864 1.0 -0.047343 0.796 0 0 -0.112992 2.386685 med 3.512786 3.625778 5.832897 3.446212 3.568835 4.483458 +Pyruvic_acid 0.016539 0.811502 1.0 -0.212837 1.01153 0 0 -0.57825 2.716869 med 29.219182 31.936051 30.489745 29.911495 30.547427 30.199236 +L-Asparagine 0.077673 0.588663 -0.337812 1.055314 0 0 -0.839365 2.484712 med 13.751007 16.161935 14.590372 13.677223 14.907813 14.126421 +L-Tryptophan -0.041416 0.603384 -0.389154 0.971701 0 0 -1.010695 2.597159 med 26.14293 27.605347 28.740089 26.594652 26.864189 27.646567
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example1_metadata.csv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,5 @@ +name_to_plot condition timepoint timenum compartment original_name +sgLDHA_T0-1 sgLDHA T0 0 endo T0_A_1 +sgLDHA_T0-2 sgLDHA T0 0 endo T0_A_2 +sgLDHA_T24-1 sgLDHA T24 24 endo T24_A_1 +sgLDHA_T24-2 sgLDHA T24 24 endo T24_A_2 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example2_metadata.csv Thu Feb 15 12:53:48 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/example3_metadata.csv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,19 @@ +name_to_plot condition timepoint timenum compartment original_name +Ctrl_cell_T0h-1 Control T0h 0 cell Sample1 +Ctrl_cell_T0h-2 Control T0h 0 cell Sample2 +Ctrl_cell_T0h-3 Control T0h 0 cell Sample3 +Ctrl_cell_T2h-1 Control T2h 2 cell Sample4 +Ctrl_cell_T2h-2 Control T2h 2 cell Sample5 +Ctrl_cell_T2h-3 Control T2h 2 cell Sample6 +Cond1_cell_T0h-1 Cond1 T0h 0 cell Sample7 +Cond1_cell_T0h-2 Cond1 T0h 0 cell Sample8 +Cond1_cell_T0h-3 Cond1 T0h 0 cell Sample9 +Cond1_cell_T2h-1 Cond1 T2h 2 cell Sample10 +Cond1_cell_T2h-2 Cond1 T2h 2 cell Sample11 +Cond1_cell_T2h-3 Cond1 T2h 2 cell Sample12 +Cond2_cell_T0h-1 Cond2 T0h 0 cell Sample13 +Cond2_cell_T0h-2 Cond2 T0h 0 cell Sample14 +Cond2_cell_T0h-3 Cond2 T0h 0 cell Sample15 +Cond2_cell_T2h-1 Cond2 T2h 2 cell Sample16 +Cond2_cell_T2h-2 Cond2 T2h 2 cell Sample17 +Cond2_cell_T2h-3 Cond2 T2h 2 cell Sample18 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example5_metadata.csv Thu Feb 15 12:53:48 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 12:53:48 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 12:53:48 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 12:53:48 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 12:53:48 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 12:53:48 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 12:53:48 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 12:53:48 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 12:53:48 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]
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathways_kegg_metabolites.csv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,8 @@ +"CENTRAL_CARBON_METABOLISM" "AMINOACIDS" +"Fumaric_acid" "L-Glutamine" +"Citric_acid" "L-Asparagine" +"Hexose" "L-Aspartic_acid" +"L-Lactic_acid" "L-Glutamic_acid" +"Pyruvic_acid" "L-Glutamine" +"Hexose-phosphate" "L-Proline" + "L-Alanine"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathways_kegg_transcripts.csv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,12 @@ +"CENTRAL_CARBON_METABOLISM" "AMINOACIDS" +"ALDOA" "ADSS1" +"GPI" "AGXT" +"PCK1" "ASL" +"PGAM1" "ASNS" +"PKM" "ASPA" +"IDH1" "GAD1" +"MDH2" "GLS" +"PC" "GLUD1" +"SDHA" "GLUD2" +"SUCLG1" +"SUCLG2"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rawAbundances.csv Thu Feb 15 12:53:48 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rawAbundances3.csv Thu Feb 15 12:53:48 2024 +0000 @@ -0,0 +1,7 @@ +ID Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9 Sample10 Sample11 Sample12 Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 +Fumaric_acid +Glycine 31339.848144444444 39953.502358333335 25011.070372222222 1867.879408333334 2173.435886666666 1221.041376190477 115741.494772222224 125731.819858333336 182398.016666666 560.116666667 19650482.416666664 656.516666666 35768152.41666667 21132662.81666667 21540901.71666667 22233782.916666664 26243782.873465 26439782.65765756 +Hexose 15263.525582222223 10653.204421666667 17620.2662477777785 2194.176071666667 3284.639177333334 2131.811518095239 6702.562494444444 6744.364736666666 5678.643333334 24242428.643333334 22336054.643333334 22906432.643333334 23957348.643333334 23850557.643333334 26889340.643333334 25837975.643333334 31838775.948787 29134981.16455938 +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-Glutamine 8606.32958888889 9863.261441666667 9512.041427777778 18956.960391666667 18701.497033333335 15374.547080952381 4094.7460777777783 4858.299791666668 +L-Tryptophan 4101.068422222223 4813.902566666667 4571.5729777777774 2610.923316666667 2975.5369333333333 2079.1386666666667 32157.056777777778 32678.538611666667 293656601.733333334 24177093.733333334 23401859.733333334 19146747.733333334 22572464.733333334 20887438.733333334 20532655.733333334 21681238.733333334 19681235.1976875 21681931.65426354 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rawAbundances_5.csv Thu Feb 15 12:53:48 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