Mercurial > repos > iuc > dimet_timecourse_analysis
changeset 0:cb8c4ae59da9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dimet_timecourse_analysis.xml Tue Oct 10 11:54:05 2023 +0000 @@ -0,0 +1,271 @@ +<tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description> + Differential analysis of tracer metabolomics data comparing consecutive time-points (by DIMet) + </description> + <macros> + <token name="@TOOL_LABEL@">timecourse analysis</token> + <token name="@EXECUTABLE@">timecourse_analysis</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + @INIT_CONFIG@ + @INIT_DIFF_ANALYSIS@ + @INIT_STAT_TEST@ + @INIT_GROUPS@ + @INIT_CONDITIONS_TIMECOURSE@ + HYDRA_FULL_ERROR=1 python -m dimet + -cp '$__new_file_path__/config' + '++figure_path=figures' + '++table_path=tables' + '++hydra.run.dir=time_course_analysis' + '++analysis={ + dataset:{ + _target_: dimet.data.DatasetConfig, + name: "I am a synthetic data example" + }, + method:{ + _target_: dimet.method.TimeCourseAnalysisConfig, + label: "time_course_analysis", + name: "Time wise computation of statistical differences" + }, + label: time_course_analysis-example + }' + '++analysis.method.qualityDistanceOverSpan='${qualityDistanceOverSpan}'' + '++analysis.statistical_test=${statistical_test}' + '++analysis.method.statistical_test=${statistical_test}' + '++analysis.method.grouping=${groups}' + '++analysis.method.correction_method=${correction_method}' + '++analysis.method.impute_values=${impute_values}' + '++analysis.dataset.subfolder=' + '++analysis.dataset.label=' + '++analysis.dataset.conditions=${conds}' + #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_diff_analysis"/> + <expand macro="conditions"/> + <expand macro="correction_method"/> + <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/> + </inputs> + <outputs> + <collection name="report" type="list"> + <discover_datasets pattern="__designation__" directory="tables" format="tabular"/> + </collection> + </outputs> + <tests> + <test> + <param name="data_input_selector" value="abundance" /> + <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/> + <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/> + <param name="correction_method" value="bonferroni"/> + <param name="qualityDistanceOverSpan" value="-0.3"/> + <param name="stat_test" value="Tt"/> + <param name="conditions" value='Control,L-Cycloserine'/> + <output_collection name="report" type="list" count="4"> + <element file="abundance--cell-Control-T2h-Control-T0-Tt.tsv" name="abundance--cell-Control-T2h-Control-T0-Tt.tsv" ftype="tabular"/> + <element file="abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" name="abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/> + <element file="abundance--med-Control-T2h-Control-T0-Tt.tsv" name="abundance--med-Control-T2h-Control-T0-Tt.tsv" ftype="tabular"/> + <element file="abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" name="abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/> + </output_collection> + + </test> + </tests> + <help><![CDATA[ +This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/). + + **Input data files** + +This tool performs a time course differential analysis on your time series data. +For illustration see the section **Metadata File Information** which contains several time points. + +This time course differential analysis is sequential: by each individual condition, a comparison between the timepoints t_x+1 vs t_x +(e.g. [Control, 90min] vs [Control, 60min]), for all the timepoints present in the data. +Our tool automatically detects the conditions and timepoints, and automatically organizes the comparisons +(you do not need to set this part yourself, DIMet does it for you). + +Note that if you need only to compare specific [condition, timepoint] pairs not comprised by +our automatic time course analysis, you can use the differential analysis in the pairwise mode instead. + + +This tool requires (at max.) 5 tab-delimited .csv files as inputs. There are two types of files: + +- The measures' (or quantifications') files, that can be of 4 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 total **abundances** (of the metabolites) file + +- The mean **enrichment** or labelled fractional contributions + +- The **isotopologues** absolute values files (optional) + +- The **isotopologue proportions** file (optional) + +and one metadata file, WHICH IS COMPULSORY, see section **Metadata File Information**. + +The measure's 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 - **Isotopologues** + + =============== ================== ================== ================== ================== ================== ================== + ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06** + =============== ================== ================== ================== ================== ================== ================== + 2_3-PG_m+0 206171.4626 285834.0353 36413.27637 27367.17784 6171.4626 119999 + 2_3-PG_m+1 123 432 101 127 206171.4626 119999 + 2_3-PG_m+2 133780.182 161461.2364 182631.3947 132170.3807 358749.348 848754.36 + 2_3-PG_m+3 8358749.348 10271010.45 10505228.3 8376820.028 62163.30727 1088.8963 + 2-OHGLu_m+0 5550339.322 6072872.833 3855047.791 3216178.72 8358749.348 10271010.45 + 2-OHGLu_m+1 0.0 0.0 0.0 0.0 206171.4626 285834.0353 + =============== ================== ================== ================== ================== ================== ================== + + +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** + -------------------- --------------- ------------- ------------ ---------------- ----------------- + Spleen1_cell_0-1 Spleen1 0min 0 cell MCF001089_TD01 + Spleen1_cell_0-2 Spleen1 0min 0 cell MCF001089_TD02 + Spleen1_cell_10-1 Spleen1 10min 10 cell MCF001089_TD03 + Spleen1_cell_10-2 Spleen1 10min 10 cell MCF001089_TD04 + Spleen1_cell_30-1 Spleen1 30min 30 cell MCF001089_TD05 + Spleen1_cell_30-2 Spleen1 30min 30 cell MCF001089_TD06 + Spleen1_cell_60-1 Spleen1 60min 60 cell MCF001089_TD07 + Spleen1_cell_60-2 Spleen1 60min 60 cell MCF001089_TD08 + Spleen1_cell_90-1 Spleen1 90min 90 cell MCF001089_TD09 + Spleen1_cell_90-2 Spleen1 90min 90 cell MCF001089_TD011 + Spleen1_med_30-3 Spleen1 30min 30 med MCF001089_TD025 + Spleen1_med_30-2 Spleen1 30min 30 med MCF001089_TD023 + ==================== =============== ============= ============ ================ ================= + + +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 + +- **statistical_test** : choose, by type of measure, the specific statistical test to be applied. + + Kruskal-Wallis, Mann-Whitney, Wilcoxon’s signed rank test, Wilcoxon’s rank sum test + t-test, and permutation test are currently offered (we use the trusted functions from scipy library https://docs.scipy.org/doc/scipy/reference/stats.html). + +For the permutation test, we have established as test statistic, the absolute difference of geometric means of the two compared groups. + +- **qualityDistanceOverSpan**: a normalized distance between the intervals of values of the compared groups, that is the cutoff for considering a minimal acceptable "separation". A 'distance/span' == 1 is a perfect separation, whereas if 'distance/span' < 0 there is no separation. To use with caution in case of important dispersion of your intra-group values. Default is -0.3 (not stringent) + +- **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). + +There exist hints on use that will guide you, next to the parameters. + +The output consists of tables with the computed metrics, one by each pair of timepoints compared. +The number of output tables = number-of-conditions x (number-of-timepoints)-1 x number-of-compartments. + +**Available data for testing** + +You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent +files for you are located in the subfolders inside the data folder). +You can also use the minimal data examples from https://zenodo.org/record/8380706 + + ]]> + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 10 11:54:05 2023 +0000 @@ -0,0 +1,778 @@ +<macros> + <token name="@TOOL_VERSION@">0.1.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@EXECUTABLE@">pca</token> + <xml name="factor_repeat"> + <repeat name="rep_factorName" title="Factor" min="1"> + <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> + <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <yield/> + </repeat> + </repeat> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> + </requirements> + </xml> + <xml name="statistical_test"> + <param name="stat_test" type="select" value="Tt" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> + <option value="Tt">t-test</option> + <option value="MW">Mann Whitney</option> + <option value="KW">Kruskall Wallis</option> + <option value="ranksum">Wilcoxon's rank sum test</option> + <option value="Wcox">Wilcoxon signed-rank test</option> + <option value="BrMu">Brunner-Munzel test</option> + <option value="prm-scipy">permutations test</option> + <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option> + </param> + </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 count 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> + </param> + <when value="abundance"> + <expand macro="abundance_file_macros"/> + <param name="metabolites_list" type="select" optional="false" multiple="true" + label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> + <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 factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> + <validator type="length" min="1" message="Please enter at max 2 compartments"/> + <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_diff_analysis"> + <conditional name="data_input"> + <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance and mean enrichment files"> + <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="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 metabolite 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="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if two conditions are set.)"> + <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"> + <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 factor 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list"> + <validator type="length" min="1" message="Please enter at max 2 compartments"/> + <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 factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> + <validator type="length" min="1" message="Please enter at max 2 compartments"/> + <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 max 2 compartments"/> + <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"> + <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"/> + </repeat> + </xml> + <token name="@INIT_PCA@"><![CDATA[ + #import json + #import re + + mkdir -p data/raw && + mkdir -p data/processed && + + #if $metadata_path: + ln -s '$metadata_path' data/raw/metadata.csv && + #end if + #if $abundance_file: + ln -s '$abundance_file' data/raw/abundance.csv && + #end if + #if $me_or_frac_contrib_file: + ln -s '$me_or_frac_contrib_file' data/raw/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/raw && + mkdir -p data/processed && + + #if $metadata_path: + ln -s '$metadata_path' data/raw/metadata.csv && + #end if + #if $abundance_file: + ln -s '$abundance_file' data/raw/abundance.csv && + #end if + ]]></token> + <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[ + + mkdir -p data/raw && + mkdir -p data/processed && + + #if $metadata_path: + ln -s '$metadata_path' data/raw/metadata.csv && + #end if + #if $me_or_frac_contrib_file: + ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && + #end if + ]]></token> + <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[ + + mkdir -p data/raw && + mkdir -p data/processed && + + #if $metadata_path: + ln -s '$metadata_path' data/raw/metadata.csv && + #end if + #if $isotop_prop_file: + ln -s '$isotop_prop_file' data/raw/isotop_prop.csv && + #end if + ]]></token> + <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[ + + mkdir -p data/raw && + mkdir -p data/processed && + + #if $metadata_path: + ln -s '$metadata_path' data/raw/metadata.csv && + #end if + + #set $impute_values = {} + #if str( $data_input.data_input_selector ) == "abundance": + #if $data_input.abundance_file: + ln -s '$data_input.abundance_file' data/raw/abundance.csv && + #silent $impute_values['abundances']='min' + #end if + #elif str( $data_input.data_input_selector ) == "mean_enrichment": + #if $data_input.me_or_frac_contrib_file: + ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && + #silent $impute_values['mean_enrichment']='min' + #end if + #elif str( $data_input.data_input_selector ) == "isotop_prop": + #if $data_input.isotop_prop_file: + ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv && + #silent $impute_values['isotopologue_proportions']='min' + #end if + #else + #if $data_input.isotop_abs_file: + ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv && + #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/raw && + mkdir -p data/processed && + mkdir -p data/integration_files && + + #if $path_kegg_metabolites: + ln -s '$path_kegg_metabolites' data/integration_files/pathways_kegg_metabolites.csv && + #end if + #if $path_kegg_transcripts: + ln -s '$path_kegg_transcripts' data/integration_files/pathways_kegg_transcripts.csv && + #end if + + #if $metadata_path: + ln -s '$metadata_path' data/raw/metadata.csv && + #end if + + #set $impute_values = {} + #if str( $data_input.data_input_selector ) == "abundance": + #if $data_input.abundance_file: + ln -s '$data_input.abundance_file' data/raw/abundance.csv && + #silent $impute_values['abundances']='min' + #end if + #else: + #if $data_input.me_or_frac_contrib_file: + ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && + #silent $impute_values['mean_enrichment']='min' + #end if + #end if + + #for $i, $s in enumerate($deg_list) + #set $cpt = str($i+1) + ln -s '${s.input}' data/integration_files/DEG_comparison'${cpt}'.csv && + #end for + + + ]]></token> + <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[ + + mkdir -p data/raw && + mkdir -p data/processed && + + #if $metadata_path: + ln -s '$metadata_path' data/raw/metadata.csv && + #end if + + #set $impute_values = {} + #if str( $data_input.data_input_selector ) == "abundance": + #if $data_input.abundance_file: + ln -s '$data_input.abundance_file' data/raw/abundance.csv && + #silent $impute_values['abundances']='min' + #end if + #elif str( $data_input.data_input_selector ) == "mean_enrichment": + #if $data_input.me_or_frac_contrib_file: + ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && + #silent $impute_values['mean_enrichment']='min' + #end if + #elif str( $data_input.data_input_selector ) == "isotop_prop": + #if $data_input.isotop_prop_file: + ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv && + #silent $impute_values['isotopologue_proportions']='min' + #end if + #else + #if $data_input.isotop_abs_file: + ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv && + #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_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: + $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str($met))) + #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 $conds = list() + #for $co in $conditions: + $conds.append(re.sub('"', '', str($co))) + #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_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/abundance--cell--multigroup.tsv Tue Oct 10 11:54:05 2023 +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-T0-L-Cycloserine-T0-Tt.tsv Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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-T0-L-Cycloserine-T0-Tt.tsv Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathways_kegg_metabolites.csv Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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 Tue Oct 10 11:54:05 2023 +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 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