Plot drug set enrichment

plotDrugSetEnrichment(
  sets,
  stats,
  col = "rankProduct_rank",
  selectedSets = NULL,
  keyColSets = NULL,
  keyColStats = NULL
)

Arguments

sets: Named list of characters: named sets containing compound identifiers (obtain drug sets by running prepareDrugSets())
stats: Named numeric vector or either a similarPerturbations or a targetingDrugs object (obtained after running rankSimilarPerturbations or predictTargetingDrugs, respectively)
col: Character: name of the column to use for statistics (only required if class of stats is either similarPerturbations or targetingDrugs)
selectedSets: Character: drug sets to plot (if NULL, plot all)
keyColSets: Character: column from sets to compare with column keyColStats from stats; automatically selected if NULL
keyColStats: Character: column from stats to compare with column keyColSets from sets; automatically selected if NULL

Value

List of GSEA plots per drug set

Examples

descriptors <- loadDrugDescriptors()
drugSets <- prepareDrugSets(descriptors)

# Analyse drug set enrichment in ranked targeting drugs for a differential
# expression profile
data("diffExprStat")
gdsc      <- loadExpressionDrugSensitivityAssociation("GDSC")
#> Loading data from expressionDrugSensitivityCorGDSC7.qs...
predicted <- predictTargetingDrugs(diffExprStat, gdsc)
#> Subsetting data based on 11396 intersecting genes (85% of the 13451 input genes)...
#> Comparing against 266 GDSC 7 compounds (983 cell lines) using 'spearman, pearson, gsea' (gene size of 150)...
#> Comparison performed in 2.58 secs

plotDrugSetEnrichment(drugSets, predicted)
#> Matching compounds with those available in drug sets...
#> Columns 'name' and 'name' were matched based on 56 common values; to manually select columns to compare, please set arguments starting with 'keyCol'
#> Plotting enrichment analysis...
#> $`FDA_status: Clinical trial`

#> 
#> $`FDA_status: FDA approved`

#> 
#> $`Mutagenic: high`

#> 
#> $`Mutagenic: low`

#> 
#> $`Mutagenic: none`

#> 
#> $`Tumorigenic: high`

#> 
#> $`Tumorigenic: low`

#> 
#> $`Tumorigenic: none`

#> 
#> $`Reproductive Effective: high`

#> 
#> $`Reproductive Effective: low`

#> 
#> $`Reproductive Effective: none`

#> 
#> $`Irritant: high`

#> 
#> $`Irritant: low`

#> 
#> $`Irritant: none`

#> 
#> $`Stereo Configuration: meso`

#> 
#> $`Stereo Configuration: racemate`

#> 
#> $`Stereo Configuration: this enantiomer`

#> 
#> $`Stereo Configuration: unknown chirality`

#> 
#> $`compound: [1, 85235]`

#> 
#> $`compound: [85236, 226080]`

#> 
#> $`compound: [226798, 601346]`

#> 
#> $`compound: [601347, 628540]`

#> 
#> $`compound: [628559, 642317]`

#> 
#> $`compound: [642319, 657194]`

#> 
#> $`compound: [657195, 669254]`

#> 
#> $`compound: [669257, 678359]`

#> 
#> $`compound: [678360, 689532]`

#> 
#> $`compound: [689533, 700034]`

#> 
#> $`compound: [700086, 711103]`

#> 
#> $`compound: [711104, 722804]`

#> 
#> $`compound: [722812, 735441]`

#> 
#> $`compound: [735444, 755892]`

#> 
#> $`compound: [755900, 783538]`

#> 
#> $`Total Molweight: [76, 240]`

#> 
#> $`Total Molweight: [241, 270]`

#> 
#> $`Total Molweight: [271, 293]`

#> 
#> $`Total Molweight: [294, 312]`

#> 
#> $`Total Molweight: [313, 332]`

#> 
#> $`Total Molweight: [333, 353]`

#> 
#> $`Total Molweight: [354, 371]`

#> 
#> $`Total Molweight: [372, 392]`

#> 
#> $`Total Molweight: [393, 414]`

#> 
#> $`Total Molweight: [415, 439]`

#> 
#> $`Total Molweight: [440, 469]`

#> 
#> $`Total Molweight: [470, 505]`

#> 
#> $`Total Molweight: [506, 557]`

#> 
#> $`Total Molweight: [558, 654]`

#> 
#> $`Total Molweight: [655, 3046]`

#> 
#> $`Monoisotopic Mass: [63, 234]`

#> 
#> $`Monoisotopic Mass: [235, 265]`

#> 
#> $`Monoisotopic Mass: [266, 287]`

#> 
#> $`Monoisotopic Mass: [288, 306]`

#> 
#> $`Monoisotopic Mass: [307, 325]`

#> 
#> $`Monoisotopic Mass: [326, 344]`

#> 
#> $`Monoisotopic Mass: [345, 363]`

#> 
#> $`Monoisotopic Mass: [364, 382]`

#> 
#> $`Monoisotopic Mass: [383, 403]`

#> 
#> $`Monoisotopic Mass: [404, 427]`

#> 
#> $`Monoisotopic Mass: [428, 456]`

#> 
#> $`Monoisotopic Mass: [457, 493]`

#> 
#> $`Monoisotopic Mass: [494, 544]`

#> 
#> $`Monoisotopic Mass: [545, 634]`

#> 
#> $`Monoisotopic Mass: [635, 3044]`

#> 
#> $`cLogP: [-28, -2]`

#> 
#> $`cLogP: -1`

#> 
#> $`cLogP: 0`

#> 
#> $`cLogP: 1`

#> 
#> $`cLogP: 2`

#> 
#> $`cLogP: 3`

#> 
#> $`cLogP: 4`

#> 
#> $`cLogP: 5`

#> 
#> $`cLogP: 6`

#> 
#> $`cLogP: 7`

#> 
#> $`cLogP: [8, 43]`

#> 
#> $`cLogS: [-35, -10]`

#> 
#> $`cLogS: -9`

#> 
#> $`cLogS: -8`

#> 
#> $`cLogS: -7`

#> 
#> $`cLogS: -6`

#> 
#> $`cLogS: -5`

#> 
#> $`cLogS: -4`

#> 
#> $`cLogS: -3`

#> 
#> $`cLogS: -2`

#> 
#> $`cLogS: [-1, 15]`

#> 
#> $`H-Acceptors: [0, 1]`

#> 
#> $`H-Acceptors: 2`

#> 
#> $`H-Acceptors: 3`

#> 
#> $`H-Acceptors: 4`

#> 
#> $`H-Acceptors: 5`

#> 
#> $`H-Acceptors: 6`

#> 
#> $`H-Acceptors: 7`

#> 
#> $`H-Acceptors: 8`

#> 
#> $`H-Acceptors: 9`

#> 
#> $`H-Acceptors: 10`

#> 
#> $`H-Acceptors: [11, 13]`

#> 
#> $`H-Acceptors: [14, 88]`

#> 
#> $`H-Donors: 0`

#> 
#> $`H-Donors: 1`

#> 
#> $`H-Donors: 2`

#> 
#> $`H-Donors: 3`

#> 
#> $`H-Donors: 4`

#> 
#> $`H-Donors: 5`

#> 
#> $`H-Donors: [6, 40]`

#> 
#> $`Total Surface Area: [26, 170]`

#> 
#> $`Total Surface Area: [171, 193]`

#> 
#> $`Total Surface Area: [194, 210]`

#> 
#> $`Total Surface Area: [211, 224]`

#> 
#> $`Total Surface Area: [225, 238]`

#> 
#> $`Total Surface Area: [239, 251]`

#> 
#> $`Total Surface Area: [252, 265]`

#> 
#> $`Total Surface Area: [266, 279]`

#> 
#> $`Total Surface Area: [280, 294]`

#> 
#> $`Total Surface Area: [295, 312]`

#> 
#> $`Total Surface Area: [313, 332]`

#> 
#> $`Total Surface Area: [333, 358]`

#> 
#> $`Total Surface Area: [359, 393]`

#> 
#> $`Total Surface Area: [394, 461]`

#> 
#> $`Total Surface Area: [462, 2109]`

#> 
#> $`Polar Surface Area: [0, 28]`

#> 
#> $`Polar Surface Area: [29, 40]`

#> 
#> $`Polar Surface Area: [41, 49]`

#> 
#> $`Polar Surface Area: [50, 57]`

#> 
#> $`Polar Surface Area: [58, 64]`

#> 
#> $`Polar Surface Area: [65, 71]`

#> 
#> $`Polar Surface Area: [72, 77]`

#> 
#> $`Polar Surface Area: [78, 84]`

#> 
#> $`Polar Surface Area: [85, 92]`

#> 
#> $`Polar Surface Area: [93, 100]`

#> 
#> $`Polar Surface Area: [101, 110]`

#> 
#> $`Polar Surface Area: [111, 122]`

#> 
#> $`Polar Surface Area: [123, 141]`

#> 
#> $`Polar Surface Area: [142, 173]`

#> 
#> $`Polar Surface Area: [174, 1251]`

#> 
#> $`Druglikeness: [-144, -15]`

#> 
#> $`Druglikeness: [-14, -9]`

#> 
#> $`Druglikeness: [-8, -7]`

#> 
#> $`Druglikeness: [-6, -5]`

#> 
#> $`Druglikeness: -4`

#> 
#> $`Druglikeness: -3`

#> 
#> $`Druglikeness: -2`

#> 
#> $`Druglikeness: -1`

#> 
#> $`Druglikeness: 0`

#> 
#> $`Druglikeness: 1`

#> 
#> $`Druglikeness: 2`

#> 
#> $`Druglikeness: 3`

#> 
#> $`Druglikeness: 4`

#> 
#> $`Druglikeness: [5, 12]`

#> 
#> $`Shape Index: 0`

#> 
#> $`Shape Index: 1`

#> 
#> $`Molecular Flexibility: 0`

#> 
#> $`Molecular Flexibility: 1`

#> 
#> $`Molecular Complexity: [0, 2]`

#> 
#> $`Fragments: 1`

#> 
#> $`Fragments: [2, 6]`

#> 
#> $`Non-H Atoms: [3, 14]`

#> 
#> $`Non-H Atoms: [15, 17]`

#> 
#> $`Non-H Atoms: [18, 19]`

#> 
#> $`Non-H Atoms: [20, 21]`

#> 
#> $`Non-H Atoms: 22`

#> 
#> $`Non-H Atoms: 23`

#> 
#> $`Non-H Atoms: 24`

#> 
#> $`Non-H Atoms: [25, 26]`

#> 
#> $`Non-H Atoms: [27, 28]`

#> 
#> $`Non-H Atoms: [29, 30]`

#> 
#> $`Non-H Atoms: [31, 32]`

#> 
#> $`Non-H Atoms: [33, 35]`

#> 
#> $`Non-H Atoms: [36, 39]`

#> 
#> $`Non-H Atoms: [40, 46]`

#> 
#> $`Non-H Atoms: [47, 202]`

#> 
#> $`Non-C/H Atoms: [0, 2]`

#> 
#> $`Non-C/H Atoms: 3`

#> 
#> $`Non-C/H Atoms: 4`

#> 
#> $`Non-C/H Atoms: 5`

#> 
#> $`Non-C/H Atoms: 6`

#> 
#> $`Non-C/H Atoms: 7`

#> 
#> $`Non-C/H Atoms: 8`

#> 
#> $`Non-C/H Atoms: 9`

#> 
#> $`Non-C/H Atoms: 10`

#> 
#> $`Non-C/H Atoms: 11`

#> 
#> $`Non-C/H Atoms: [12, 13]`

#> 
#> $`Non-C/H Atoms: [14, 108]`

#> 
#> $`Metal-Atoms: 0`

#> 
#> $`Metal-Atoms: [1, 4]`

#> 
#> $`Electronegative Atoms: [0, 2]`

#> 
#> $`Electronegative Atoms: 3`

#> 
#> $`Electronegative Atoms: 4`

#> 
#> $`Electronegative Atoms: 5`

#> 
#> $`Electronegative Atoms: 6`

#> 
#> $`Electronegative Atoms: 7`

#> 
#> $`Electronegative Atoms: 8`

#> 
#> $`Electronegative Atoms: 9`

#> 
#> $`Electronegative Atoms: 10`

#> 
#> $`Electronegative Atoms: [11, 12]`

#> 
#> $`Electronegative Atoms: [13, 108]`

#> 
#> $`Stereo Centers: 0`

#> 
#> $`Stereo Centers: 1`

#> 
#> $`Stereo Centers: 2`

#> 
#> $`Stereo Centers: 3`

#> 
#> $`Stereo Centers: 4`

#> 
#> $`Stereo Centers: 5`

#> 
#> $`Stereo Centers: 6`

#> 
#> $`Stereo Centers: [7, 8]`

#> 
#> $`Stereo Centers: [9, 11]`

#> 
#> $`Stereo Centers: [12, 50]`

#> 
#> $`Rotatable Bonds: 0`

#> 
#> $`Rotatable Bonds: 1`

#> 
#> $`Rotatable Bonds: 2`

#> 
#> $`Rotatable Bonds: 3`

#> 
#> $`Rotatable Bonds: 4`

#> 
#> $`Rotatable Bonds: 5`

#> 
#> $`Rotatable Bonds: 6`

#> 
#> $`Rotatable Bonds: 7`

#> 
#> $`Rotatable Bonds: 8`

#> 
#> $`Rotatable Bonds: [9, 10]`

#> 
#> $`Rotatable Bonds: [11, 13]`

#> 
#> $`Rotatable Bonds: [14, 89]`

#> 
#> $`Rings Closures: 0`

#> 
#> $`Rings Closures: 1`

#> 
#> $`Rings Closures: 2`

#> 
#> $`Rings Closures: 3`

#> 
#> $`Rings Closures: 4`

#> 
#> $`Rings Closures: 5`

#> 
#> $`Rings Closures: 6`

#> 
#> $`Rings Closures: 7`

#> 
#> $`Rings Closures: [8, 38]`

#> 
#> $`Small Rings: 0`

#> 
#> $`Small Rings: 1`

#> 
#> $`Small Rings: 2`

#> 
#> $`Small Rings: 3`

#> 
#> $`Small Rings: 4`

#> 
#> $`Small Rings: 5`

#> 
#> $`Small Rings: 6`

#> 
#> $`Small Rings: 7`

#> 
#> $`Small Rings: 8`

#> 
#> $`Small Rings: [9, 289]`

#> 
#> $`Aromatic Rings: 0`

#> 
#> $`Aromatic Rings: 1`

#> 
#> $`Aromatic Rings: 2`

#> 
#> $`Aromatic Rings: 3`

#> 
#> $`Aromatic Rings: 4`

#> 
#> $`Aromatic Rings: 5`

#> 
#> $`Aromatic Rings: [6, 15]`

#> 
#> $`Aromatic Atoms: 0`

#> 
#> $`Aromatic Atoms: 5`

#> 
#> $`Aromatic Atoms: 6`

#> 
#> $`Aromatic Atoms: [8, 10]`

#> 
#> $`Aromatic Atoms: 11`

#> 
#> $`Aromatic Atoms: 12`

#> 
#> $`Aromatic Atoms: [13, 14]`

#> 
#> $`Aromatic Atoms: 15`

#> 
#> $`Aromatic Atoms: 16`

#> 
#> $`Aromatic Atoms: 17`

#> 
#> $`Aromatic Atoms: 18`

#> 
#> $`Aromatic Atoms: [19, 20]`

#> 
#> $`Aromatic Atoms: [21, 22]`

#> 
#> $`Aromatic Atoms: [23, 24]`

#> 
#> $`Aromatic Atoms: [25, 78]`

#> 
#> $`sp3-Atoms: 0`

#> 
#> $`sp3-Atoms: 1`

#> 
#> $`sp3-Atoms: 2`

#> 
#> $`sp3-Atoms: 3`

#> 
#> $`sp3-Atoms: 4`

#> 
#> $`sp3-Atoms: 5`

#> 
#> $`sp3-Atoms: 6`

#> 
#> $`sp3-Atoms: 7`

#> 
#> $`sp3-Atoms: 8`

#> 
#> $`sp3-Atoms: 9`

#> 
#> $`sp3-Atoms: [10, 11]`

#> 
#> $`sp3-Atoms: [12, 13]`

#> 
#> $`sp3-Atoms: [14, 16]`

#> 
#> $`sp3-Atoms: [17, 22]`

#> 
#> $`sp3-Atoms: [23, 126]`

#> 
#> $`Symmetric atoms: 0`

#> 
#> $`Symmetric atoms: 1`

#> 
#> $`Symmetric atoms: 2`

#> 
#> $`Symmetric atoms: 3`

#> 
#> $`Symmetric atoms: 4`

#> 
#> $`Symmetric atoms: 5`

#> 
#> $`Symmetric atoms: 6`

#> 
#> $`Symmetric atoms: 7`

#> 
#> $`Symmetric atoms: 8`

#> 
#> $`Symmetric atoms: [9, 10]`

#> 
#> $`Symmetric atoms: [11, 12]`

#> 
#> $`Symmetric atoms: [13, 14]`

#> 
#> $`Symmetric atoms: [15, 17]`

#> 
#> $`Symmetric atoms: [18, 22]`

#> 
#> $`Symmetric atoms: [23, 122]`

#> 
#> $`Amides: 0`

#> 
#> $`Amides: 1`

#> 
#> $`Amides: 2`

#> 
#> $`Amides: [3, 22]`

#> 
#> $`Amines: 0`

#> 
#> $`Amines: 1`

#> 
#> $`Amines: 2`

#> 
#> $`Amines: [3, 10]`

#> 
#> $`Alkyl-Amines: 0`

#> 
#> $`Alkyl-Amines: 1`

#> 
#> $`Alkyl-Amines: [2, 10]`

#> 
#> $`Aromatic Amines: 0`

#> 
#> $`Aromatic Amines: 1`

#> 
#> $`Aromatic Amines: [2, 6]`

#> 
#> $`Aromatic Nitrogens: 0`

#> 
#> $`Aromatic Nitrogens: 1`

#> 
#> $`Aromatic Nitrogens: 2`

#> 
#> $`Aromatic Nitrogens: 3`

#> 
#> $`Aromatic Nitrogens: [4, 12]`

#> 
#> $`Basic Nitrogens: 0`

#> 
#> $`Basic Nitrogens: 1`

#> 
#> $`Basic Nitrogens: 2`

#> 
#> $`Basic Nitrogens: [3, 10]`

#> 
#> $`Acidic Oxygens: 0`

#> 
#> $`Acidic Oxygens: 1`

#> 
#> $`Acidic Oxygens: [2, 9]`

#>

Plot drug set enrichment

Arguments

Value

See also

Examples