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

See also

Other functions for drug set enrichment analysis: analyseDrugSetEnrichment(), loadDrugDescriptors(), prepareDrugSets()

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 3 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`

#> 
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#> $`Irritant: none`

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

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#> 
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#> 
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#> 
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#> 
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#> 
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#> 
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#> 
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#> 
#> $`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]`

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

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

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

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

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

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

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

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

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#> $`Druglikeness: -3`

#> 
#> $`Druglikeness: -2`

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#> $`Druglikeness: -1`

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#> $`Druglikeness: 0`

#> 
#> $`Druglikeness: 1`

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#> $`Druglikeness: 2`

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#> $`Druglikeness: 3`

#> 
#> $`Druglikeness: 4`

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

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#> $`Shape Index: 1`

#> 
#> $`Molecular Flexibility: 0`

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#> $`Molecular Flexibility: 1`

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

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

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

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

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#> $`Non-H Atoms: 24`

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

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

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

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

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#> $`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]`

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

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#> $`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]`

#> 
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#> 
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#> 
#> $`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`

#> 
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#> 
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#> 
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#> 
#> $`Stereo Centers: 0`

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#> 
#> $`Rotatable Bonds: 5`

#> 
#> $`Rotatable Bonds: 6`

#> 
#> $`Rotatable Bonds: 7`

#> 
#> $`Rotatable Bonds: 8`

#> 
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#> 
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#> 
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#> $`Small Rings: 1`

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#> $`Small Rings: 2`

#> 
#> $`Small Rings: 3`

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#> $`Small Rings: 4`

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#> $`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]`

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

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#> 
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#> 
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#> 
#> $`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]`

#> 
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#> 
#> $`Amides: 1`

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

#> 
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#> 
#> $`Amines: 1`

#> 
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#> 
#> $`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]`

#>