{ "cells": [ { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " levelName SetID Identifier WSEntry\n", "1 plants 1 PlantID plant\n", "2 °--samples 2 SampleID sample\n", "3 ¦--aliquots 3 AliquotID aliquot\n", "4 ¦ ¦--cellwall_metabo 4 AliquotID aliquot\n", "5 ¦ ¦--cellwall_metaboFW 5 AliquotID aliquot\n", "6 ¦ ¦--activome 6 AliquotID aliquot\n", "7 ¦ ¦--plato_hexosesP 10 AliquotID aliquot\n", "8 ¦ ¦--lipids_AG 11 AliquotID aliquot\n", "9 ¦ °--AminoAcid 12 AliquotID aliquot\n", "10 °--pools 7 PoolID pool\n", "11 ¦--qMS_metabo 8 PoolID pool\n", "12 °--qNMR_metabo 9 PoolID pool\n", " Description Count\n", "1 Plant features 552\n", "2 Sample features 1288\n", "3 Aliquots features 530\n", "4 Cell wall Compound quantifications 75\n", "5 Cell Wall Compound quantifications (FW) 75\n", "6 Activome Features 266\n", "7 Hexoses Phosphate 266\n", "8 Lipids AG 57\n", "9 Amino Acids 69\n", "10 Pools of remaining pools 195\n", "11 MS Compounds quantification 25\n", "12 NMR Compounds quantification 64\n" ] } ], "source": [ "library(Rodam)\n", "\n", "# Initialize the 'ODAM' object \n", "dh <- new('odamws', 'http://pmb-bordeaux.fr/getdata/', 'frim1')\n", "\n", "# Get the Data Tree\n", "show(dh)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
    \n", "\t
  1. 'plants'
    2. \n", "\t
  2. 'samples'
    3. \n", "\t
  3. 'aliquots'
    4. \n", "\t
  4. 'cellwall_metabo'
    5. \n", "\t
  5. 'cellwall_metaboFW'
    6. \n", "\t
  6. 'activome'
    7. \n", "\t
  7. 'pools'
    8. \n", "\t
  8. 'qMS_metabo'
    9. \n", "\t
  9. 'qNMR_metabo'
    10. \n", "\t
  10. 'plato_hexosesP'
    11. \n", "\t
  11. 'lipids_AG'
    12. \n", "\t
  12. 'AminoAcid'
    13. \n", "
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 'plants'\n", "\\item 'samples'\n", "\\item 'aliquots'\n", "\\item 'cellwall\\_metabo'\n", "\\item 'cellwall\\_metaboFW'\n", "\\item 'activome'\n", "\\item 'pools'\n", "\\item 'qMS\\_metabo'\n", "\\item 'qNMR\\_metabo'\n", "\\item 'plato\\_hexosesP'\n", "\\item 'lipids\\_AG'\n", "\\item 'AminoAcid'\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 'plants'\n", "2. 'samples'\n", "3. 'aliquots'\n", "4. 'cellwall_metabo'\n", "5. 'cellwall_metaboFW'\n", "6. 'activome'\n", "7. 'pools'\n", "8. 'qMS_metabo'\n", "9. 'qNMR_metabo'\n", "10. 'plato_hexosesP'\n", "11. 'lipids_AG'\n", "12. 'AminoAcid'\n", "\n", "\n" ], "text/plain": [ " [1] \"plants\" \"samples\" \"aliquots\" \n", " [4] \"cellwall_metabo\" \"cellwall_metaboFW\" \"activome\" \n", " [7] \"pools\" \"qMS_metabo\" \"qNMR_metabo\" \n", "[10] \"plato_hexosesP\" \"lipids_AG\" \"AminoAcid\" " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Get the data subsets list\n", "dh$subsetNames" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A data.frame: 42 × 6
SubsetAttributeDescriptionTypeCV_Term_ID CV_Term_Name
<chr><chr><chr><chr><chr><chr>
activomeAliquotID Aliquot Identifier Identifierhttp://edamontology.org/data_0842 identifier
plants Treatment Treatment applied on plants Factor http://www.ebi.ac.uk/efo/EFO_0000469 environmental factor
samples DevStage fruit development stage Factor http://purl.obolibrary.org/obo/PO_0001002fruit development stage
samples FruitAge fruit age (dpa) Factor http://purl.obolibrary.org/obo/PO_0001002fruit development stage
activomePGM Phosphoglucomutase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004614EC 5.4.2.2 Phosphoglucomutase
activomecFBPase cytosolic Fru-1,6-bisphosphatase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0042132EC 3.1.3.11 fructose-bisphosphatase
activomePyrK Pyruvate Kinase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004743EC 2.7.1.40 pyruvate kinase
activomeCitS Citrate Synthase Total (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0036440EC 2.3.3.1 citrate synthase
activomePPI PPI (nmol/gFW/min) Variable
activomeAconitase Aconitase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_000394 EC 4.2.1.3 Aconitase
activomePFK ATP-Phosphofructokinase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0008443EC 2.7.1.11 phosphofructokinase
activomeFruK Fructokinase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0008865EC 2.7.1.4 fructokinase
activomepFBPase plastidial Fru-1,6-bisphosphatase (nmol/gFW/min)Variable http://purl.obolibrary.org/obo/GO_0042132EC 3.1.3.11 fructose-bisphosphatase
activomeGluK Glucokinase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004340EC 2.7.1.2 Glucokinase
activomeNAD_ISODH Isocitrate DH - NADP (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004450EC 1.1.1.42 isocitrate dehydrogenase
activomeEnolase Enolase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0000015EC 4.2.1.11 Enolase
activomeNADP_ISODH Isocitrate DH - NAD (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004448EC 1.1.1.41 isocitrate dehydrogenase
activomePEPC PEP Carboxylase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0008964EC 4.1.1.31 PEP Carboxylase
activomeAldolase FBP-Aldolase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004332EC 4.1.2.13 fructose-bisphosphate aldolase
activomeSucc_CoA_ligaseSuccinate CoA ligase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0042709EC 6.2.1.5 Succinate CoA ligase
activomeNAD_MalDH Malate DH - NAD (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0016615EC 1.1.1.37 malate dehydrogenase
activomeAlaAT Alanine aminotransferase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004021EC 2.6.1.2 alanine transaminase
activomeFumarase Fumarase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004333EC 4.2.1.2 fumarase
activomeAspAT Aspartate aminotransferase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004069EC 2.6.1.1 aspartate aminotransferase
activomeNADP_GluDH Glutamate DH - NADP (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004354EC 1.4.1.4 glutamate dehydrogenase NADP
activomeNAD_GAPDH GAPDH - NAD (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004365EC 1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase NAD
activomeNADP_GAPDH GAPDH - NADP (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0047100EC 1.2.1.13 glyceraldehyde-3-phosphate dehydrogenase NADP
activomeNAD_GluDH Glutamate DH - NAD (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004352EC 1.4.1.2 glutamate dehydrogenase NAP
activomeTPI Triose Phosphate Isomerase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004807EC 5.3.1.1 triose-phosphate isomerase
activomePGK Phosphoglycerokinase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004618EC 2.7.2.3 phosphoglycerate kinase
activomeNeutral_Inv Neutral invertase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004564EC 3.2.1.26 invertase
activomeAcid_Inv Acid invertase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004564EC 3.2.1.26 invertase
activomeG6PDH Glucose-6-Phosphate Dehydrogenase (nmol/gFW/min)Variable http://purl.obolibrary.org/obo/GO_0004345EC 1.1.1.49 glucose-6-phosphate dehydrogenase
activomeUGPase UDP-Glucose Pyrophosphorylase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0003983EC 2.7.7.9 UDPG phosphorylase
activomeSuSy Sucrose Synthase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0016157EC 2.4.1.13 sucrose synthase
activomeNAD_ME Malic Enzyme NAD (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0009763EC 1.1.1.38 NAD+-malic enzyme
activomeShiDH Shikimate dehydrogenase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0033706EC 1.1.1.282 shikimate dehydrogenase
activomeNADP_ME Malic Enzyme NADP (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0009762EC 1.1.1.40 NADP+-malic enzyme
activomePGI Phosphoglucose Isomerase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0004347EC 5.3.1.9 phosphohexose isomerase
activomeStarchS Soluble Starch Synthase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0009011EC 2.4.1.21 starch synthase
activomeAGPase AGPase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0080042EC 2.7.7.27 ADP-glucose synthase
activomeSPS Sucrose Phosphate Synthase (nmol/gFW/min) Variable http://purl.obolibrary.org/obo/GO_0046524EC 2.4.1.14 sucrose-phosphate synthase
\n" ], "text/latex": [ "A data.frame: 42 × 6\n", "\\begin{tabular}{llllll}\n", " Subset & Attribute & Description & Type & CV\\_Term\\_ID & CV\\_Term\\_Name\\\\\n", " & & & & & \\\\\n", "\\hline\n", "\t activome & AliquotID & Aliquot Identifier & Identifier & http://edamontology.org/data\\_0842 & identifier \\\\\n", "\t plants & Treatment & Treatment applied on plants & Factor & http://www.ebi.ac.uk/efo/EFO\\_0000469 & environmental factor \\\\\n", "\t samples & DevStage & fruit development stage & Factor & http://purl.obolibrary.org/obo/PO\\_0001002 & fruit development stage \\\\\n", "\t samples & FruitAge & fruit age (dpa) & Factor & http://purl.obolibrary.org/obo/PO\\_0001002 & fruit development stage \\\\\n", "\t activome & PGM & Phosphoglucomutase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004614 & EC 5.4.2.2 Phosphoglucomutase \\\\\n", "\t activome & cFBPase & cytosolic Fru-1,6-bisphosphatase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0042132 & EC 3.1.3.11 fructose-bisphosphatase \\\\\n", "\t activome & PyrK & Pyruvate Kinase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004743 & EC 2.7.1.40 pyruvate kinase \\\\\n", "\t activome & CitS & Citrate Synthase Total (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0036440 & EC 2.3.3.1 citrate synthase \\\\\n", "\t activome & PPI & PPI (nmol/gFW/min) & Variable & & \\\\\n", "\t activome & Aconitase & Aconitase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_000394 & EC 4.2.1.3 Aconitase \\\\\n", "\t activome & PFK & ATP-Phosphofructokinase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0008443 & EC 2.7.1.11 phosphofructokinase \\\\\n", "\t activome & FruK & Fructokinase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0008865 & EC 2.7.1.4 fructokinase \\\\\n", "\t activome & pFBPase & plastidial Fru-1,6-bisphosphatase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0042132 & EC 3.1.3.11 fructose-bisphosphatase \\\\\n", "\t activome & GluK & Glucokinase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004340 & EC 2.7.1.2 Glucokinase \\\\\n", "\t activome & NAD\\_ISODH & Isocitrate DH - NADP (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004450 & EC 1.1.1.42 isocitrate dehydrogenase \\\\\n", "\t activome & Enolase & Enolase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0000015 & EC 4.2.1.11 Enolase \\\\\n", "\t activome & NADP\\_ISODH & Isocitrate DH - NAD (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004448 & EC 1.1.1.41 isocitrate dehydrogenase \\\\\n", "\t activome & PEPC & PEP Carboxylase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0008964 & EC 4.1.1.31 PEP Carboxylase \\\\\n", "\t activome & Aldolase & FBP-Aldolase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004332 & EC 4.1.2.13 fructose-bisphosphate aldolase \\\\\n", "\t activome & Succ\\_CoA\\_ligase & Succinate CoA ligase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0042709 & EC 6.2.1.5 Succinate CoA ligase \\\\\n", "\t activome & NAD\\_MalDH & Malate DH - NAD (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0016615 & EC 1.1.1.37 malate dehydrogenase \\\\\n", "\t activome & AlaAT & Alanine aminotransferase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004021 & EC 2.6.1.2 alanine transaminase \\\\\n", "\t activome & Fumarase & Fumarase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004333 & EC 4.2.1.2 fumarase \\\\\n", "\t activome & AspAT & Aspartate aminotransferase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004069 & EC 2.6.1.1 aspartate aminotransferase \\\\\n", "\t activome & NADP\\_GluDH & Glutamate DH - NADP (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004354 & EC 1.4.1.4 glutamate dehydrogenase NADP \\\\\n", "\t activome & NAD\\_GAPDH & GAPDH - NAD (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004365 & EC 1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase NAD \\\\\n", "\t activome & NADP\\_GAPDH & GAPDH - NADP (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0047100 & EC 1.2.1.13 glyceraldehyde-3-phosphate dehydrogenase NADP\\\\\n", "\t activome & NAD\\_GluDH & Glutamate DH - NAD (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004352 & EC 1.4.1.2 glutamate dehydrogenase NAP \\\\\n", "\t activome & TPI & Triose Phosphate Isomerase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004807 & EC 5.3.1.1 triose-phosphate isomerase \\\\\n", "\t activome & PGK & Phosphoglycerokinase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004618 & EC 2.7.2.3 phosphoglycerate kinase \\\\\n", "\t activome & Neutral\\_Inv & Neutral invertase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004564 & EC 3.2.1.26 invertase \\\\\n", "\t activome & Acid\\_Inv & Acid invertase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004564 & EC 3.2.1.26 invertase \\\\\n", "\t activome & G6PDH & Glucose-6-Phosphate Dehydrogenase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004345 & EC 1.1.1.49 glucose-6-phosphate dehydrogenase \\\\\n", "\t activome & UGPase & UDP-Glucose Pyrophosphorylase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0003983 & EC 2.7.7.9 UDPG phosphorylase \\\\\n", "\t activome & SuSy & Sucrose Synthase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0016157 & EC 2.4.1.13 sucrose synthase \\\\\n", "\t activome & NAD\\_ME & Malic Enzyme NAD (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0009763 & EC 1.1.1.38 NAD+-malic enzyme \\\\\n", "\t activome & ShiDH & Shikimate dehydrogenase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0033706 & EC 1.1.1.282 shikimate dehydrogenase \\\\\n", "\t activome & NADP\\_ME & Malic Enzyme NADP (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0009762 & EC 1.1.1.40 NADP+-malic enzyme \\\\\n", "\t activome & PGI & Phosphoglucose Isomerase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0004347 & EC 5.3.1.9 phosphohexose isomerase \\\\\n", "\t activome & StarchS & Soluble Starch Synthase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0009011 & EC 2.4.1.21 starch synthase \\\\\n", "\t activome & AGPase & AGPase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0080042 & EC 2.7.7.27 ADP-glucose synthase \\\\\n", "\t activome & SPS & Sucrose Phosphate Synthase (nmol/gFW/min) & Variable & http://purl.obolibrary.org/obo/GO\\_0046524 & EC 2.4.1.14 sucrose-phosphate synthase \\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A data.frame: 42 × 6\n", "\n", "| Subset <chr> | Attribute <chr> | Description <chr> | Type <chr> | CV_Term_ID <chr> | CV_Term_Name <chr> |\n", "|---|---|---|---|---|---|\n", "| activome | AliquotID | Aliquot Identifier | Identifier | http://edamontology.org/data_0842 | identifier |\n", "| plants | Treatment | Treatment applied on plants | Factor | http://www.ebi.ac.uk/efo/EFO_0000469 | environmental factor |\n", "| samples | DevStage | fruit development stage | Factor | http://purl.obolibrary.org/obo/PO_0001002 | fruit development stage |\n", "| samples | FruitAge | fruit age (dpa) | Factor | http://purl.obolibrary.org/obo/PO_0001002 | fruit development stage |\n", "| activome | PGM | Phosphoglucomutase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004614 | EC 5.4.2.2 Phosphoglucomutase |\n", "| activome | cFBPase | cytosolic Fru-1,6-bisphosphatase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0042132 | EC 3.1.3.11 fructose-bisphosphatase |\n", "| activome | PyrK | Pyruvate Kinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004743 | EC 2.7.1.40 pyruvate kinase |\n", "| activome | CitS | Citrate Synthase Total (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0036440 | EC 2.3.3.1 citrate synthase |\n", "| activome | PPI | PPI (nmol/gFW/min) | Variable | | |\n", "| activome | Aconitase | Aconitase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_000394 | EC 4.2.1.3 Aconitase |\n", "| activome | PFK | ATP-Phosphofructokinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0008443 | EC 2.7.1.11 phosphofructokinase |\n", "| activome | FruK | Fructokinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0008865 | EC 2.7.1.4 fructokinase |\n", "| activome | pFBPase | plastidial Fru-1,6-bisphosphatase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0042132 | EC 3.1.3.11 fructose-bisphosphatase |\n", "| activome | GluK | Glucokinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004340 | EC 2.7.1.2 Glucokinase |\n", "| activome | NAD_ISODH | Isocitrate DH - NADP (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004450 | EC 1.1.1.42 isocitrate dehydrogenase |\n", "| activome | Enolase | Enolase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0000015 | EC 4.2.1.11 Enolase |\n", "| activome | NADP_ISODH | Isocitrate DH - NAD (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004448 | EC 1.1.1.41 isocitrate dehydrogenase |\n", "| activome | PEPC | PEP Carboxylase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0008964 | EC 4.1.1.31 PEP Carboxylase |\n", "| activome | Aldolase | FBP-Aldolase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004332 | EC 4.1.2.13 fructose-bisphosphate aldolase |\n", "| activome | Succ_CoA_ligase | Succinate CoA ligase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0042709 | EC 6.2.1.5 Succinate CoA ligase |\n", "| activome | NAD_MalDH | Malate DH - NAD (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0016615 | EC 1.1.1.37 malate dehydrogenase |\n", "| activome | AlaAT | Alanine aminotransferase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004021 | EC 2.6.1.2 alanine transaminase |\n", "| activome | Fumarase | Fumarase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004333 | EC 4.2.1.2 fumarase |\n", "| activome | AspAT | Aspartate aminotransferase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004069 | EC 2.6.1.1 aspartate aminotransferase |\n", "| activome | NADP_GluDH | Glutamate DH - NADP (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004354 | EC 1.4.1.4 glutamate dehydrogenase NADP |\n", "| activome | NAD_GAPDH | GAPDH - NAD (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004365 | EC 1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase NAD |\n", "| activome | NADP_GAPDH | GAPDH - NADP (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0047100 | EC 1.2.1.13 glyceraldehyde-3-phosphate dehydrogenase NADP |\n", "| activome | NAD_GluDH | Glutamate DH - NAD (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004352 | EC 1.4.1.2 glutamate dehydrogenase NAP |\n", "| activome | TPI | Triose Phosphate Isomerase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004807 | EC 5.3.1.1 triose-phosphate isomerase |\n", "| activome | PGK | Phosphoglycerokinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004618 | EC 2.7.2.3 phosphoglycerate kinase |\n", "| activome | Neutral_Inv | Neutral invertase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004564 | EC 3.2.1.26 invertase |\n", "| activome | Acid_Inv | Acid invertase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004564 | EC 3.2.1.26 invertase |\n", "| activome | G6PDH | Glucose-6-Phosphate Dehydrogenase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004345 | EC 1.1.1.49 glucose-6-phosphate dehydrogenase |\n", "| activome | UGPase | UDP-Glucose Pyrophosphorylase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0003983 | EC 2.7.7.9 UDPG phosphorylase |\n", "| activome | SuSy | Sucrose Synthase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0016157 | EC 2.4.1.13 sucrose synthase |\n", "| activome | NAD_ME | Malic Enzyme NAD (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0009763 | EC 1.1.1.38 NAD+-malic enzyme |\n", "| activome | ShiDH | Shikimate dehydrogenase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0033706 | EC 1.1.1.282 shikimate dehydrogenase |\n", "| activome | NADP_ME | Malic Enzyme NADP (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0009762 | EC 1.1.1.40 NADP+-malic enzyme |\n", "| activome | PGI | Phosphoglucose Isomerase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004347 | EC 5.3.1.9 phosphohexose isomerase |\n", "| activome | StarchS | Soluble Starch Synthase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0009011 | EC 2.4.1.21 starch synthase |\n", "| activome | AGPase | AGPase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0080042 | EC 2.7.7.27 ADP-glucose synthase |\n", "| activome | SPS | Sucrose Phosphate Synthase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0046524 | EC 2.4.1.14 sucrose-phosphate synthase |\n", "\n" ], "text/plain": [ " Subset Attribute Description \n", "1 activome AliquotID Aliquot Identifier \n", "2 plants Treatment Treatment applied on plants \n", "3 samples DevStage fruit development stage \n", "4 samples FruitAge fruit age (dpa) \n", "5 activome PGM Phosphoglucomutase (nmol/gFW/min) \n", "6 activome cFBPase cytosolic Fru-1,6-bisphosphatase (nmol/gFW/min) \n", "7 activome PyrK Pyruvate Kinase (nmol/gFW/min) \n", "8 activome CitS Citrate Synthase Total (nmol/gFW/min) \n", "9 activome PPI PPI (nmol/gFW/min) \n", "10 activome Aconitase Aconitase (nmol/gFW/min) \n", "11 activome PFK ATP-Phosphofructokinase (nmol/gFW/min) \n", "12 activome FruK Fructokinase (nmol/gFW/min) \n", "13 activome pFBPase plastidial Fru-1,6-bisphosphatase (nmol/gFW/min)\n", "14 activome GluK Glucokinase (nmol/gFW/min) \n", "15 activome NAD_ISODH Isocitrate DH - NADP (nmol/gFW/min) \n", "16 activome Enolase Enolase (nmol/gFW/min) \n", "17 activome NADP_ISODH Isocitrate DH - NAD (nmol/gFW/min) \n", "18 activome PEPC PEP Carboxylase (nmol/gFW/min) \n", "19 activome Aldolase FBP-Aldolase (nmol/gFW/min) \n", "20 activome Succ_CoA_ligase Succinate CoA ligase (nmol/gFW/min) \n", "21 activome NAD_MalDH Malate DH - NAD (nmol/gFW/min) \n", "22 activome AlaAT Alanine aminotransferase (nmol/gFW/min) \n", "23 activome Fumarase Fumarase (nmol/gFW/min) \n", "24 activome AspAT Aspartate aminotransferase (nmol/gFW/min) \n", "25 activome NADP_GluDH Glutamate DH - NADP (nmol/gFW/min) \n", "26 activome NAD_GAPDH GAPDH - NAD (nmol/gFW/min) \n", "27 activome NADP_GAPDH GAPDH - NADP (nmol/gFW/min) \n", "28 activome NAD_GluDH Glutamate DH - NAD (nmol/gFW/min) \n", "29 activome TPI Triose Phosphate Isomerase (nmol/gFW/min) \n", "30 activome PGK Phosphoglycerokinase (nmol/gFW/min) \n", "31 activome Neutral_Inv Neutral invertase (nmol/gFW/min) \n", "32 activome Acid_Inv Acid invertase (nmol/gFW/min) \n", "33 activome G6PDH Glucose-6-Phosphate Dehydrogenase (nmol/gFW/min)\n", "34 activome UGPase UDP-Glucose Pyrophosphorylase (nmol/gFW/min) \n", "35 activome SuSy Sucrose Synthase (nmol/gFW/min) \n", "36 activome NAD_ME Malic Enzyme NAD (nmol/gFW/min) \n", "37 activome ShiDH Shikimate dehydrogenase (nmol/gFW/min) \n", "38 activome NADP_ME Malic Enzyme NADP (nmol/gFW/min) \n", "39 activome PGI Phosphoglucose Isomerase (nmol/gFW/min) \n", "40 activome StarchS Soluble Starch Synthase (nmol/gFW/min) \n", "41 activome AGPase AGPase (nmol/gFW/min) \n", "42 activome SPS Sucrose Phosphate Synthase (nmol/gFW/min) \n", " Type CV_Term_ID \n", "1 Identifier http://edamontology.org/data_0842 \n", "2 Factor http://www.ebi.ac.uk/efo/EFO_0000469 \n", "3 Factor http://purl.obolibrary.org/obo/PO_0001002\n", "4 Factor http://purl.obolibrary.org/obo/PO_0001002\n", "5 Variable http://purl.obolibrary.org/obo/GO_0004614\n", "6 Variable http://purl.obolibrary.org/obo/GO_0042132\n", "7 Variable http://purl.obolibrary.org/obo/GO_0004743\n", "8 Variable http://purl.obolibrary.org/obo/GO_0036440\n", "9 Variable \n", "10 Variable http://purl.obolibrary.org/obo/GO_000394 \n", "11 Variable http://purl.obolibrary.org/obo/GO_0008443\n", "12 Variable http://purl.obolibrary.org/obo/GO_0008865\n", "13 Variable http://purl.obolibrary.org/obo/GO_0042132\n", "14 Variable http://purl.obolibrary.org/obo/GO_0004340\n", "15 Variable http://purl.obolibrary.org/obo/GO_0004450\n", "16 Variable http://purl.obolibrary.org/obo/GO_0000015\n", "17 Variable http://purl.obolibrary.org/obo/GO_0004448\n", "18 Variable http://purl.obolibrary.org/obo/GO_0008964\n", "19 Variable http://purl.obolibrary.org/obo/GO_0004332\n", "20 Variable http://purl.obolibrary.org/obo/GO_0042709\n", "21 Variable http://purl.obolibrary.org/obo/GO_0016615\n", "22 Variable http://purl.obolibrary.org/obo/GO_0004021\n", "23 Variable http://purl.obolibrary.org/obo/GO_0004333\n", "24 Variable http://purl.obolibrary.org/obo/GO_0004069\n", "25 Variable http://purl.obolibrary.org/obo/GO_0004354\n", "26 Variable http://purl.obolibrary.org/obo/GO_0004365\n", "27 Variable http://purl.obolibrary.org/obo/GO_0047100\n", "28 Variable http://purl.obolibrary.org/obo/GO_0004352\n", "29 Variable http://purl.obolibrary.org/obo/GO_0004807\n", "30 Variable http://purl.obolibrary.org/obo/GO_0004618\n", "31 Variable http://purl.obolibrary.org/obo/GO_0004564\n", "32 Variable http://purl.obolibrary.org/obo/GO_0004564\n", "33 Variable http://purl.obolibrary.org/obo/GO_0004345\n", "34 Variable http://purl.obolibrary.org/obo/GO_0003983\n", "35 Variable http://purl.obolibrary.org/obo/GO_0016157\n", "36 Variable http://purl.obolibrary.org/obo/GO_0009763\n", "37 Variable http://purl.obolibrary.org/obo/GO_0033706\n", "38 Variable http://purl.obolibrary.org/obo/GO_0009762\n", "39 Variable http://purl.obolibrary.org/obo/GO_0004347\n", "40 Variable http://purl.obolibrary.org/obo/GO_0009011\n", "41 Variable http://purl.obolibrary.org/obo/GO_0080042\n", "42 Variable http://purl.obolibrary.org/obo/GO_0046524\n", " CV_Term_Name \n", "1 identifier \n", "2 environmental factor \n", "3 fruit development stage \n", "4 fruit development stage \n", "5 EC 5.4.2.2 Phosphoglucomutase \n", "6 EC 3.1.3.11 fructose-bisphosphatase \n", "7 EC 2.7.1.40 pyruvate kinase \n", "8 EC 2.3.3.1 citrate synthase \n", "9 \n", "10 EC 4.2.1.3 Aconitase \n", "11 EC 2.7.1.11 phosphofructokinase \n", "12 EC 2.7.1.4 fructokinase \n", "13 EC 3.1.3.11 fructose-bisphosphatase \n", "14 EC 2.7.1.2 Glucokinase \n", "15 EC 1.1.1.42 isocitrate dehydrogenase \n", "16 EC 4.2.1.11 Enolase \n", "17 EC 1.1.1.41 isocitrate dehydrogenase \n", "18 EC 4.1.1.31 PEP Carboxylase \n", "19 EC 4.1.2.13 fructose-bisphosphate aldolase \n", "20 EC 6.2.1.5 Succinate CoA ligase \n", "21 EC 1.1.1.37 malate dehydrogenase \n", "22 EC 2.6.1.2 alanine transaminase \n", "23 EC 4.2.1.2 fumarase \n", "24 EC 2.6.1.1 aspartate aminotransferase \n", "25 EC 1.4.1.4 glutamate dehydrogenase NADP \n", "26 EC 1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase NAD \n", "27 EC 1.2.1.13 glyceraldehyde-3-phosphate dehydrogenase NADP\n", "28 EC 1.4.1.2 glutamate dehydrogenase NAP \n", "29 EC 5.3.1.1 triose-phosphate isomerase \n", "30 EC 2.7.2.3 phosphoglycerate kinase \n", "31 EC 3.2.1.26 invertase \n", "32 EC 3.2.1.26 invertase \n", "33 EC 1.1.1.49 glucose-6-phosphate dehydrogenase \n", "34 EC 2.7.7.9 UDPG phosphorylase \n", "35 EC 2.4.1.13 sucrose synthase \n", "36 EC 1.1.1.38 NAD+-malic enzyme \n", "37 EC 1.1.1.282 shikimate dehydrogenase \n", "38 EC 1.1.1.40 NADP+-malic enzyme \n", "39 EC 5.3.1.9 phosphohexose isomerase \n", "40 EC 2.4.1.21 starch synthase \n", "41 EC 2.7.7.27 ADP-glucose synthase \n", "42 EC 2.4.1.14 sucrose-phosphate synthase " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Get 'activome' data subset\n", "ds <- dh$getSubsetByName('activome')\n", "\n", "# Show all descriptions of variables\n", "ds$LABELS" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
    \n", "\t
  1. 'Treatment'
    2. \n", "\t
  2. 'DevStage'
    3. \n", "\t
  3. 'FruitAge'
    4. \n", "
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 'Treatment'\n", "\\item 'DevStage'\n", "\\item 'FruitAge'\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 'Treatment'\n", "2. 'DevStage'\n", "3. 'FruitAge'\n", "\n", "\n" ], "text/plain": [ "[1] \"Treatment\" \"DevStage\" \"FruitAge\" " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Show all factors defined in the data subset\n", "ds$facnames" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
    \n", "\t
  1. 'PGM'
    2. \n", "\t
  2. 'cFBPase'
    3. \n", "\t
  3. 'PyrK'
    4. \n", "\t
  4. 'CitS'
    5. \n", "\t
  5. 'PPI'
    6. \n", "\t
  6. 'Aconitase'
    7. \n", "\t
  7. 'PFK'
    8. \n", "\t
  8. 'FruK'
    9. \n", "\t
  9. 'pFBPase'
    10. \n", "\t
  10. 'GluK'
    11. \n", "\t
  11. 'NAD_ISODH'
    12. \n", "\t
  12. 'Enolase'
    13. \n", "\t
  13. 'NADP_ISODH'
    14. \n", "\t
  14. 'PEPC'
    15. \n", "\t
  15. 'Aldolase'
    16. \n", "\t
  16. 'Succ_CoA_ligase'
    17. \n", "\t
  17. 'NAD_MalDH'
    18. \n", "\t
  18. 'AlaAT'
    19. \n", "\t
  19. 'Fumarase'
    20. \n", "\t
  20. 'AspAT'
    21. \n", "\t
  21. 'NADP_GluDH'
    22. \n", "\t
  22. 'NAD_GAPDH'
    23. \n", "\t
  23. 'NADP_GAPDH'
    24. \n", "\t
  24. 'NAD_GluDH'
    25. \n", "\t
  25. 'TPI'
    26. \n", "\t
  26. 'PGK'
    27. \n", "\t
  27. 'Neutral_Inv'
    28. \n", "\t
  28. 'Acid_Inv'
    29. \n", "\t
  29. 'G6PDH'
    30. \n", "\t
  30. 'UGPase'
    31. \n", "\t
  31. 'SuSy'
    32. \n", "\t
  32. 'NAD_ME'
    33. \n", "\t
  33. 'ShiDH'
    34. \n", "\t
  34. 'NADP_ME'
    35. \n", "\t
  35. 'PGI'
    36. \n", "\t
  36. 'StarchS'
    37. \n", "\t
  37. 'AGPase'
    38. \n", "\t
  38. 'SPS'
    39. \n", "
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 'PGM'\n", "\\item 'cFBPase'\n", "\\item 'PyrK'\n", "\\item 'CitS'\n", "\\item 'PPI'\n", "\\item 'Aconitase'\n", "\\item 'PFK'\n", "\\item 'FruK'\n", "\\item 'pFBPase'\n", "\\item 'GluK'\n", "\\item 'NAD\\_ISODH'\n", "\\item 'Enolase'\n", "\\item 'NADP\\_ISODH'\n", "\\item 'PEPC'\n", "\\item 'Aldolase'\n", "\\item 'Succ\\_CoA\\_ligase'\n", "\\item 'NAD\\_MalDH'\n", "\\item 'AlaAT'\n", "\\item 'Fumarase'\n", "\\item 'AspAT'\n", "\\item 'NADP\\_GluDH'\n", "\\item 'NAD\\_GAPDH'\n", "\\item 'NADP\\_GAPDH'\n", "\\item 'NAD\\_GluDH'\n", "\\item 'TPI'\n", "\\item 'PGK'\n", "\\item 'Neutral\\_Inv'\n", "\\item 'Acid\\_Inv'\n", "\\item 'G6PDH'\n", "\\item 'UGPase'\n", "\\item 'SuSy'\n", "\\item 'NAD\\_ME'\n", "\\item 'ShiDH'\n", "\\item 'NADP\\_ME'\n", "\\item 'PGI'\n", "\\item 'StarchS'\n", "\\item 'AGPase'\n", "\\item 'SPS'\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 'PGM'\n", "2. 'cFBPase'\n", "3. 'PyrK'\n", "4. 'CitS'\n", "5. 'PPI'\n", "6. 'Aconitase'\n", "7. 'PFK'\n", "8. 'FruK'\n", "9. 'pFBPase'\n", "10. 'GluK'\n", "11. 'NAD_ISODH'\n", "12. 'Enolase'\n", "13. 'NADP_ISODH'\n", "14. 'PEPC'\n", "15. 'Aldolase'\n", "16. 'Succ_CoA_ligase'\n", "17. 'NAD_MalDH'\n", "18. 'AlaAT'\n", "19. 'Fumarase'\n", "20. 'AspAT'\n", "21. 'NADP_GluDH'\n", "22. 'NAD_GAPDH'\n", "23. 'NADP_GAPDH'\n", "24. 'NAD_GluDH'\n", "25. 'TPI'\n", "26. 'PGK'\n", "27. 'Neutral_Inv'\n", "28. 'Acid_Inv'\n", "29. 'G6PDH'\n", "30. 'UGPase'\n", "31. 'SuSy'\n", "32. 'NAD_ME'\n", "33. 'ShiDH'\n", "34. 'NADP_ME'\n", "35. 'PGI'\n", "36. 'StarchS'\n", "37. 'AGPase'\n", "38. 'SPS'\n", "\n", "\n" ], "text/plain": [ " [1] \"PGM\" \"cFBPase\" \"PyrK\" \"CitS\" \n", " [5] \"PPI\" \"Aconitase\" \"PFK\" \"FruK\" \n", " [9] \"pFBPase\" \"GluK\" \"NAD_ISODH\" \"Enolase\" \n", "[13] \"NADP_ISODH\" \"PEPC\" \"Aldolase\" \"Succ_CoA_ligase\"\n", "[17] \"NAD_MalDH\" \"AlaAT\" \"Fumarase\" \"AspAT\" \n", "[21] \"NADP_GluDH\" \"NAD_GAPDH\" \"NADP_GAPDH\" \"NAD_GluDH\" \n", "[25] \"TPI\" \"PGK\" \"Neutral_Inv\" \"Acid_Inv\" \n", "[29] \"G6PDH\" \"UGPase\" \"SuSy\" \"NAD_ME\" \n", "[33] \"ShiDH\" \"NADP_ME\" \"PGI\" \"StarchS\" \n", "[37] \"AGPase\" \"SPS\" " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Show all quantitative variables defined in the data subset\n", "ds$varnames" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/html": [], "text/latex": [], "text/markdown": [], "text/plain": [ "character(0)" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Show all qualitative variables defined in the data subset\n", "ds$qualnames" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/plain": [ " PGM cFBPase PyrK CitS \n", " Min. : 4.11 Min. : 0.02 Min. : 5.25 Min. : 0.20 \n", " 1st Qu.: 934.62 1st Qu.: 7.32 1st Qu.: 172.04 1st Qu.: 19.03 \n", " Median :1609.69 Median :10.97 Median : 276.78 Median : 33.08 \n", " Mean :2156.69 Mean :12.81 Mean : 472.99 Mean : 41.71 \n", " 3rd Qu.:3064.04 3rd Qu.:16.64 3rd Qu.: 556.97 3rd Qu.: 59.91 \n", " Max. :8054.61 Max. :85.02 Max. :3053.11 Max. :171.99 \n", " NA's :46 NA's :37 NA's :227 \n", " PPI Aconitase PFK FruK \n", " Min. : 60.49 Min. : 12.06 Min. : 8.59 Min. : 5.60 \n", " 1st Qu.: 395.51 1st Qu.: 88.30 1st Qu.: 49.27 1st Qu.: 55.94 \n", " Median : 637.17 Median : 164.71 Median : 72.59 Median : 97.51 \n", " Mean : 973.64 Mean : 308.42 Mean : 89.60 Mean : 242.68 \n", " 3rd Qu.:1364.62 3rd Qu.: 344.83 3rd Qu.:118.84 3rd Qu.: 344.62 \n", " Max. :3373.46 Max. :2014.02 Max. :270.30 Max. :1223.19 \n", " NA's :29 NA's :7 \n", " pFBPase GluK NAD_ISODH Enolase \n", " Min. : 5.28 Min. : 0.01 Min. : 52.67 Min. : 2.21 \n", " 1st Qu.: 46.90 1st Qu.: 33.44 1st Qu.:122.94 1st Qu.:226.35 \n", " Median :102.46 Median : 83.51 Median :182.58 Median :320.36 \n", " Mean :162.53 Mean : 186.81 Mean :231.85 Mean :348.46 \n", " 3rd Qu.:209.70 3rd Qu.: 271.34 3rd Qu.:284.48 3rd Qu.:503.27 \n", " Max. :778.47 Max. :1271.77 Max. :975.77 Max. :766.52 \n", " NA's :17 NA's :60 NA's :4 NA's :99 \n", " NADP_ISODH PEPC Aldolase Succ_CoA_ligase \n", " Min. : 0.27 Min. : 3.09 Min. : 215.6 Min. : 12.27 \n", " 1st Qu.: 23.32 1st Qu.: 214.94 1st Qu.: 1861.7 1st Qu.: 172.61 \n", " Median : 44.24 Median : 397.33 Median : 2683.7 Median : 268.17 \n", " Mean : 59.45 Mean : 457.07 Mean : 3440.4 Mean : 391.75 \n", " 3rd Qu.: 86.79 3rd Qu.: 672.65 3rd Qu.: 4620.1 3rd Qu.: 539.01 \n", " Max. :231.52 Max. :1414.29 Max. :11538.5 Max. :1528.87 \n", " NA's :265 NA's :16 NA's :14 \n", " NAD_MalDH AlaAT Fumarase AspAT \n", " Min. : 2178 Min. : 7.14 Min. : 10.33 Min. : 378 \n", " 1st Qu.: 8879 1st Qu.: 829.48 1st Qu.: 142.42 1st Qu.: 1828 \n", " Median :18530 Median :1263.87 Median : 290.33 Median : 2800 \n", " Mean :25507 Mean :1329.22 Mean : 420.92 Mean : 4935 \n", " 3rd Qu.:38895 3rd Qu.:1777.71 3rd Qu.: 548.57 3rd Qu.: 6471 \n", " Max. :78412 Max. :4605.69 Max. :1753.96 Max. :19862 \n", " NA's :94 NA's :241 NA's :216 \n", " NADP_GluDH NAD_GAPDH NADP_GAPDH NAD_GluDH \n", " Min. : 0.030 Min. : 244.6 Min. : 6.82 Min. : 1.16 \n", " 1st Qu.: 2.660 1st Qu.:1187.2 1st Qu.: 500.82 1st Qu.: 27.57 \n", " Median : 5.410 Median :1905.9 Median : 798.36 Median : 48.62 \n", " Mean : 5.978 Mean :2539.9 Mean :1007.51 Mean : 76.32 \n", " 3rd Qu.: 8.107 3rd Qu.:3245.1 3rd Qu.:1307.23 3rd Qu.: 81.40 \n", " Max. :22.790 Max. :9000.0 Max. :9647.29 Max. :336.56 \n", " NA's :222 NA's :26 NA's :36 NA's :115 \n", " TPI PGK Neutral_Inv Acid_Inv \n", " Min. : 2946 Min. : 301.1 Min. : 4.81 Min. :-2083.6 \n", " 1st Qu.: 27346 1st Qu.: 3635.4 1st Qu.: 57.97 1st Qu.: 40.5 \n", " Median : 51122 Median : 5492.4 Median :123.70 Median : 398.1 \n", " Mean : 77922 Mean : 7634.1 Mean :131.10 Mean : 540.6 \n", " 3rd Qu.:115730 3rd Qu.: 9884.5 3rd Qu.:190.59 3rd Qu.: 823.3 \n", " Max. :299124 Max. :27041.3 Max. :402.54 Max. : 4236.6 \n", " NA's :5 \n", " G6PDH UGPase SuSy NAD_ME \n", " Min. : 17.8 Min. :1102 Min. : 2.01 Min. : 5.3 \n", " 1st Qu.:101.8 1st Qu.:2984 1st Qu.: 228.90 1st Qu.: 414.8 \n", " Median :131.2 Median :3275 Median : 353.76 Median : 986.9 \n", " Mean :183.5 Mean :3198 Mean : 427.21 Mean :1086.3 \n", " 3rd Qu.:250.3 3rd Qu.:3538 3rd Qu.: 587.89 3rd Qu.:1608.5 \n", " Max. :678.3 Max. :4145 Max. :3130.57 Max. :3893.2 \n", " NA's :38 NA's :9 NA's :125 NA's :100 \n", " ShiDH NADP_ME PGI StarchS \n", " Min. : 3.55 Min. : 1.38 Min. : 31.37 Min. : 1.23 \n", " 1st Qu.: 67.48 1st Qu.: 89.87 1st Qu.: 356.56 1st Qu.: 40.44 \n", " Median : 98.97 Median :172.36 Median : 520.14 Median : 66.16 \n", " Mean :190.91 Mean :181.01 Mean : 702.01 Mean : 83.89 \n", " 3rd Qu.:180.13 3rd Qu.:263.44 3rd Qu.: 941.90 3rd Qu.:116.13 \n", " Max. :944.64 Max. :560.68 Max. :2392.79 Max. :256.72 \n", " NA's :4 NA's :64 NA's :57 \n", " AGPase SPS \n", " Min. : 0.73 Min. : 1.47 \n", " 1st Qu.: 257.81 1st Qu.: 52.23 \n", " Median : 409.79 Median : 83.12 \n", " Mean : 498.92 Mean :101.27 \n", " 3rd Qu.: 726.49 3rd Qu.:124.63 \n", " Max. :1372.63 Max. :678.33 \n", " NA's :35 NA's :168 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Display a summary for each quantitative variable\n", "summary(ds$data[, ds$varnames ])" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "data": { "image/png": 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"text/plain": [ "plot without title" ] }, "metadata": { "image/png": { "height": 600, "width": 720 }, "text/plain": { "height": 600, "width": 720 } }, "output_type": "display_data" } ], "source": [ "# Boxplot of all variables defined in ds$varnames\n", "Rank <- simplify2array(lapply(ds$varnames, function(x) { round(mean(log10(ds$data[ , x]), na.rm=T)) }))\n", "Rank[!is.finite(Rank)] <- 0\n", "colRank <- Rank - min(Rank) + 1\n", "cols <- c('red', 'orange', 'darkgreen', 'blue', 'purple', 'brown')\n", "options(repr.plot.width=12, repr.plot.height=10)\n", "boxplot(log10(ds$data[, ds$varnames]), outline=F, horizontal=T, border=cols[colRank], las=2, cex.axis=0.5)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "R", "language": "R", "name": "ir" }, "language_info": { "codemirror_mode": "r", "file_extension": ".r", "mimetype": "text/x-r-source", "name": "R", "pygments_lexer": "r", "version": "3.5.1" }, "nteract": { "version": "0.15.0" } }, "nbformat": 4, "nbformat_minor": 2 }