In [3]:
library(Rodam)
# Initialize the 'ODAM' object
dh <- new('odamws', 'http://pmb-bordeaux.fr/getdata/', 'frim1')
# Get the Data Tree
show(dh)
levelName SetID Identifier WSEntry
1 plants 1 PlantID plant
2 °--samples 2 SampleID sample
3 ¦--aliquots 3 AliquotID aliquot
4 ¦ ¦--cellwall_metabo 4 AliquotID aliquot
5 ¦ ¦--cellwall_metaboFW 5 AliquotID aliquot
6 ¦ ¦--activome 6 AliquotID aliquot
7 ¦ ¦--plato_hexosesP 10 AliquotID aliquot
8 ¦ ¦--lipids_AG 11 AliquotID aliquot
9 ¦ °--AminoAcid 12 AliquotID aliquot
10 °--pools 7 PoolID pool
11 ¦--qMS_metabo 8 PoolID pool
12 °--qNMR_metabo 9 PoolID pool
Description Count
1 Plant features 552
2 Sample features 1288
3 Aliquots features 530
4 Cell wall Compound quantifications 75
5 Cell Wall Compound quantifications (FW) 75
6 Activome Features 266
7 Hexoses Phosphate 266
8 Lipids AG 57
9 Amino Acids 69
10 Pools of remaining pools 195
11 MS Compounds quantification 25
12 NMR Compounds quantification 64
In [4]:
# Get the data subsets list
dh$subsetNames
- 'plants'
- 'samples'
- 'aliquots'
- 'cellwall_metabo'
- 'cellwall_metaboFW'
- 'activome'
- 'pools'
- 'qMS_metabo'
- 'qNMR_metabo'
- 'plato_hexosesP'
- 'lipids_AG'
- 'AminoAcid'
In [5]:
# Get 'activome' data subset
ds <- dh$getSubsetByName('activome')
# Show all descriptions of variables
ds$LABELS
| Subset | Attribute | Description | Type | CV_Term_ID | CV_Term_Name |
|---|---|---|---|---|---|
| <chr> | <chr> | <chr> | <chr> | <chr> | <chr> |
| activome | AliquotID | Aliquot Identifier | Identifier | http://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_0001002 | fruit development stage |
| samples | FruitAge | fruit age (dpa) | Factor | http://purl.obolibrary.org/obo/PO_0001002 | fruit development stage |
| activome | PGM | Phosphoglucomutase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004614 | EC 5.4.2.2 Phosphoglucomutase |
| 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 |
| activome | PyrK | Pyruvate Kinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004743 | EC 2.7.1.40 pyruvate kinase |
| activome | CitS | Citrate Synthase Total (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0036440 | EC 2.3.3.1 citrate synthase |
| activome | PPI | PPI (nmol/gFW/min) | Variable | ||
| activome | Aconitase | Aconitase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_000394 | EC 4.2.1.3 Aconitase |
| activome | PFK | ATP-Phosphofructokinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0008443 | EC 2.7.1.11 phosphofructokinase |
| activome | FruK | Fructokinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0008865 | EC 2.7.1.4 fructokinase |
| 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 |
| activome | GluK | Glucokinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004340 | EC 2.7.1.2 Glucokinase |
| activome | NAD_ISODH | Isocitrate DH - NADP (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004450 | EC 1.1.1.42 isocitrate dehydrogenase |
| activome | Enolase | Enolase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0000015 | EC 4.2.1.11 Enolase |
| activome | NADP_ISODH | Isocitrate DH - NAD (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004448 | EC 1.1.1.41 isocitrate dehydrogenase |
| activome | PEPC | PEP Carboxylase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0008964 | EC 4.1.1.31 PEP Carboxylase |
| activome | Aldolase | FBP-Aldolase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004332 | EC 4.1.2.13 fructose-bisphosphate aldolase |
| 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 |
| activome | NAD_MalDH | Malate DH - NAD (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0016615 | EC 1.1.1.37 malate dehydrogenase |
| activome | AlaAT | Alanine aminotransferase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004021 | EC 2.6.1.2 alanine transaminase |
| activome | Fumarase | Fumarase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004333 | EC 4.2.1.2 fumarase |
| activome | AspAT | Aspartate aminotransferase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004069 | EC 2.6.1.1 aspartate aminotransferase |
| 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 |
| 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 |
| 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 |
| 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 |
| activome | TPI | Triose Phosphate Isomerase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004807 | EC 5.3.1.1 triose-phosphate isomerase |
| activome | PGK | Phosphoglycerokinase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004618 | EC 2.7.2.3 phosphoglycerate kinase |
| activome | Neutral_Inv | Neutral invertase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004564 | EC 3.2.1.26 invertase |
| activome | Acid_Inv | Acid invertase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004564 | EC 3.2.1.26 invertase |
| 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 |
| activome | UGPase | UDP-Glucose Pyrophosphorylase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0003983 | EC 2.7.7.9 UDPG phosphorylase |
| activome | SuSy | Sucrose Synthase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0016157 | EC 2.4.1.13 sucrose synthase |
| 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 |
| activome | ShiDH | Shikimate dehydrogenase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0033706 | EC 1.1.1.282 shikimate dehydrogenase |
| 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 |
| activome | PGI | Phosphoglucose Isomerase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0004347 | EC 5.3.1.9 phosphohexose isomerase |
| activome | StarchS | Soluble Starch Synthase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0009011 | EC 2.4.1.21 starch synthase |
| activome | AGPase | AGPase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0080042 | EC 2.7.7.27 ADP-glucose synthase |
| activome | SPS | Sucrose Phosphate Synthase (nmol/gFW/min) | Variable | http://purl.obolibrary.org/obo/GO_0046524 | EC 2.4.1.14 sucrose-phosphate synthase |
In [6]:
# Show all factors defined in the data subset
ds$facnames
- 'Treatment'
- 'DevStage'
- 'FruitAge'
In [7]:
# Show all quantitative variables defined in the data subset
ds$varnames
- 'PGM'
- 'cFBPase'
- 'PyrK'
- 'CitS'
- 'PPI'
- 'Aconitase'
- 'PFK'
- 'FruK'
- 'pFBPase'
- 'GluK'
- 'NAD_ISODH'
- 'Enolase'
- 'NADP_ISODH'
- 'PEPC'
- 'Aldolase'
- 'Succ_CoA_ligase'
- 'NAD_MalDH'
- 'AlaAT'
- 'Fumarase'
- 'AspAT'
- 'NADP_GluDH'
- 'NAD_GAPDH'
- 'NADP_GAPDH'
- 'NAD_GluDH'
- 'TPI'
- 'PGK'
- 'Neutral_Inv'
- 'Acid_Inv'
- 'G6PDH'
- 'UGPase'
- 'SuSy'
- 'NAD_ME'
- 'ShiDH'
- 'NADP_ME'
- 'PGI'
- 'StarchS'
- 'AGPase'
- 'SPS'
In [8]:
# Show all qualitative variables defined in the data subset
ds$qualnames
In [9]:
# Display a summary for each quantitative variable
summary(ds$data[, ds$varnames ])
PGM cFBPase PyrK CitS
Min. : 4.11 Min. : 0.02 Min. : 5.25 Min. : 0.20
1st Qu.: 934.62 1st Qu.: 7.32 1st Qu.: 172.04 1st Qu.: 19.03
Median :1609.69 Median :10.97 Median : 276.78 Median : 33.08
Mean :2156.69 Mean :12.81 Mean : 472.99 Mean : 41.71
3rd Qu.:3064.04 3rd Qu.:16.64 3rd Qu.: 556.97 3rd Qu.: 59.91
Max. :8054.61 Max. :85.02 Max. :3053.11 Max. :171.99
NA's :46 NA's :37 NA's :227
PPI Aconitase PFK FruK
Min. : 60.49 Min. : 12.06 Min. : 8.59 Min. : 5.60
1st Qu.: 395.51 1st Qu.: 88.30 1st Qu.: 49.27 1st Qu.: 55.94
Median : 637.17 Median : 164.71 Median : 72.59 Median : 97.51
Mean : 973.64 Mean : 308.42 Mean : 89.60 Mean : 242.68
3rd Qu.:1364.62 3rd Qu.: 344.83 3rd Qu.:118.84 3rd Qu.: 344.62
Max. :3373.46 Max. :2014.02 Max. :270.30 Max. :1223.19
NA's :29 NA's :7
pFBPase GluK NAD_ISODH Enolase
Min. : 5.28 Min. : 0.01 Min. : 52.67 Min. : 2.21
1st Qu.: 46.90 1st Qu.: 33.44 1st Qu.:122.94 1st Qu.:226.35
Median :102.46 Median : 83.51 Median :182.58 Median :320.36
Mean :162.53 Mean : 186.81 Mean :231.85 Mean :348.46
3rd Qu.:209.70 3rd Qu.: 271.34 3rd Qu.:284.48 3rd Qu.:503.27
Max. :778.47 Max. :1271.77 Max. :975.77 Max. :766.52
NA's :17 NA's :60 NA's :4 NA's :99
NADP_ISODH PEPC Aldolase Succ_CoA_ligase
Min. : 0.27 Min. : 3.09 Min. : 215.6 Min. : 12.27
1st Qu.: 23.32 1st Qu.: 214.94 1st Qu.: 1861.7 1st Qu.: 172.61
Median : 44.24 Median : 397.33 Median : 2683.7 Median : 268.17
Mean : 59.45 Mean : 457.07 Mean : 3440.4 Mean : 391.75
3rd Qu.: 86.79 3rd Qu.: 672.65 3rd Qu.: 4620.1 3rd Qu.: 539.01
Max. :231.52 Max. :1414.29 Max. :11538.5 Max. :1528.87
NA's :265 NA's :16 NA's :14
NAD_MalDH AlaAT Fumarase AspAT
Min. : 2178 Min. : 7.14 Min. : 10.33 Min. : 378
1st Qu.: 8879 1st Qu.: 829.48 1st Qu.: 142.42 1st Qu.: 1828
Median :18530 Median :1263.87 Median : 290.33 Median : 2800
Mean :25507 Mean :1329.22 Mean : 420.92 Mean : 4935
3rd Qu.:38895 3rd Qu.:1777.71 3rd Qu.: 548.57 3rd Qu.: 6471
Max. :78412 Max. :4605.69 Max. :1753.96 Max. :19862
NA's :94 NA's :241 NA's :216
NADP_GluDH NAD_GAPDH NADP_GAPDH NAD_GluDH
Min. : 0.030 Min. : 244.6 Min. : 6.82 Min. : 1.16
1st Qu.: 2.660 1st Qu.:1187.2 1st Qu.: 500.82 1st Qu.: 27.57
Median : 5.410 Median :1905.9 Median : 798.36 Median : 48.62
Mean : 5.978 Mean :2539.9 Mean :1007.51 Mean : 76.32
3rd Qu.: 8.107 3rd Qu.:3245.1 3rd Qu.:1307.23 3rd Qu.: 81.40
Max. :22.790 Max. :9000.0 Max. :9647.29 Max. :336.56
NA's :222 NA's :26 NA's :36 NA's :115
TPI PGK Neutral_Inv Acid_Inv
Min. : 2946 Min. : 301.1 Min. : 4.81 Min. :-2083.6
1st Qu.: 27346 1st Qu.: 3635.4 1st Qu.: 57.97 1st Qu.: 40.5
Median : 51122 Median : 5492.4 Median :123.70 Median : 398.1
Mean : 77922 Mean : 7634.1 Mean :131.10 Mean : 540.6
3rd Qu.:115730 3rd Qu.: 9884.5 3rd Qu.:190.59 3rd Qu.: 823.3
Max. :299124 Max. :27041.3 Max. :402.54 Max. : 4236.6
NA's :5
G6PDH UGPase SuSy NAD_ME
Min. : 17.8 Min. :1102 Min. : 2.01 Min. : 5.3
1st Qu.:101.8 1st Qu.:2984 1st Qu.: 228.90 1st Qu.: 414.8
Median :131.2 Median :3275 Median : 353.76 Median : 986.9
Mean :183.5 Mean :3198 Mean : 427.21 Mean :1086.3
3rd Qu.:250.3 3rd Qu.:3538 3rd Qu.: 587.89 3rd Qu.:1608.5
Max. :678.3 Max. :4145 Max. :3130.57 Max. :3893.2
NA's :38 NA's :9 NA's :125 NA's :100
ShiDH NADP_ME PGI StarchS
Min. : 3.55 Min. : 1.38 Min. : 31.37 Min. : 1.23
1st Qu.: 67.48 1st Qu.: 89.87 1st Qu.: 356.56 1st Qu.: 40.44
Median : 98.97 Median :172.36 Median : 520.14 Median : 66.16
Mean :190.91 Mean :181.01 Mean : 702.01 Mean : 83.89
3rd Qu.:180.13 3rd Qu.:263.44 3rd Qu.: 941.90 3rd Qu.:116.13
Max. :944.64 Max. :560.68 Max. :2392.79 Max. :256.72
NA's :4 NA's :64 NA's :57
AGPase SPS
Min. : 0.73 Min. : 1.47
1st Qu.: 257.81 1st Qu.: 52.23
Median : 409.79 Median : 83.12
Mean : 498.92 Mean :101.27
3rd Qu.: 726.49 3rd Qu.:124.63
Max. :1372.63 Max. :678.33
NA's :35 NA's :168
In [12]:
# Boxplot of all variables defined in ds$varnames
Rank <- simplify2array(lapply(ds$varnames, function(x) { round(mean(log10(ds$data[ , x]), na.rm=T)) }))
Rank[!is.finite(Rank)] <- 0
colRank <- Rank - min(Rank) + 1
cols <- c('red', 'orange', 'darkgreen', 'blue', 'purple', 'brown')
options(repr.plot.width=12, repr.plot.height=10)
boxplot(log10(ds$data[, ds$varnames]), outline=F, horizontal=T, border=cols[colRank], las=2, cex.axis=0.5)
In [ ]: