gongxin8888 commented 7 months ago

Hi Dr. Yu,

Here is my code:

Serumenricher <- compareCluster(geneCluster=Serum, fun=enricher, pvalueCutoff = 1, minGSSize = 4, maxGSSize = 500, pAdjustMethod="BH", TERM2GENE=path2comp, TERM2NAME=path2Names );

Serum is a list of KEGG ID List of 7 $ blue : chr [1:20] "C16325" "C16353" "C11045" "D02381" ... $ black : chr [1:6] "D07176" "C06869" "D07614" "C01921" ... $ red : chr [1:7] "C01801" "C00486" "C02237" "C00078" ... $ brown : chr [1:12] "C16651" "C16366" "C00486" "C00486" ... $ turquoise: chr [1:19] "C01089" "C03601" "C00114" "D07690" ... $ green : chr [1:17] "C00300" "C00791" "D03600" "C17935" ... $ yellow : chr [1:12] "C11993" "C00939" "C07597" "C07597" ..

It failed with the following errors::

Error in fun(i, ...) : could not find function "fun"

Any suggestion?

Thanks

GongXin

Prerequisites

[ ] Have you read Feedback and followed the guide?
- [ ] make sure you are using the latest release version
- [ ] read the documentation
- [ ] google your quesion/issue

Describe your issue

[ ] Make a reproducible example (e.g. 1)
[ ] your code should contain comments to describe the problem (e.g. what you expected and what actually happened)

Ask in the right place

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guidohooiveld commented 7 months ago

Does it work with the example code (since your code as such is not reproducible)? What is your sessionInfo()?

> library(clusterProfiler)
> data(gcSample)
> xx <- compareCluster(gcSample, fun=enrichKEGG,
+                      organism="hsa", pvalueCutoff=0.05)
> xx
#
# Result of Comparing 8 gene clusters 
#
#.. @fun         enrichKEGG 
#.. @geneClusters       List of 8
 $ X1: chr [1:216] "4597" "7111" "5266" "2175" ...
 $ X2: chr [1:805] "23450" "5160" "7126" "26118" ...
 $ X3: chr [1:392] "894" "7057" "22906" "3339" ...
 $ X4: chr [1:838] "5573" "7453" "5245" "23450" ...
 $ X5: chr [1:929] "5982" "7318" "6352" "2101" ...
 $ X6: chr [1:585] "5337" "9295" "4035" "811" ...
 $ X7: chr [1:582] "2621" "2665" "5690" "3608" ...
 $ X8: chr [1:237] "2665" "4735" "1327" "3192" ...
#...Result      'data.frame':   76 obs. of  12 variables:
 $ Cluster    : Factor w/ 8 levels "X1","X2","X3",..: 2 2 2 3 3 3 4 4 4 4 ...
 $ category   : chr  "Human Diseases" "Human Diseases" "Cellular Processes" "Environmental Information Processing" ...
 $ subcategory: chr  "Infectious disease: viral" "Immune disease" "Cell growth and death" "Signaling molecules and interaction" ...
 $ ID         : chr  "hsa05169" "hsa05340" "hsa04110" "hsa04512" ...
 $ Description: chr  "Epstein-Barr virus infection" "Primary immunodeficiency" "Cell cycle" "ECM-receptor interaction" ...
 $ GeneRatio  : chr  "23/406" "8/406" "18/406" "9/193" ...
 $ BgRatio    : chr  "202/8662" "38/8662" "157/8662" "89/8662" ...
 $ pvalue     : num  6.83e-05 3.07e-04 3.83e-04 1.53e-04 3.29e-04 ...
 $ p.adjust   : num  0.0214 0.0399 0.0399 0.0362 0.0362 ...
 $ qvalue     : num  0.0199 0.0372 0.0372 0.0335 0.0335 ...
 $ geneID     : chr  "4067/3383/7128/1869/890/1871/578/864/637/9641/6891/355/9134/5971/916/956/6850/7187/3551/919/4734/958/6772" "100/6891/3932/973/916/925/958/64421" "991/1869/890/1871/701/990/10926/9088/8317/9700/9134/1029/2810/699/11200/23594/8555/4173" "7057/3339/1299/3695/1101/3679/3910/3696/3693" ...
 $ Count      : int  23 8 18 9 17 19 17 10 22 19 ...
#.. number of enriched terms found for each gene cluster:
#..   X1: 0 
#..   X2: 3 
#..   X3: 3 
#..   X4: 22 
#..   X5: 10 
#..   X6: 1 
#..   X7: 17 
#..   X8: 20 
#
#...Citation
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, 
W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. 
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. 
The Innovation. 2021, 2(3):100141 

>

gongxin8888 commented 7 months ago

Hi Guido,

It does work with the following example but not with fun = enricher. I found alternative where I created a customized function with enricher. With that function, it works for me.

Thanks and have a great day!

GongXin

From: Guido Hooiveld @.> Date: Thursday, February 22, 2024 at 2:05 AM To: YuLab-SMU/clusterProfiler @.> Cc: Yu, Gongxin @.>, Author @.> Subject: [EXTERNAL] [MARKETING] Re: [YuLab-SMU/clusterProfiler] problem in run compareCluster (Issue #669)

Does it work with the example code (since your code as such is not reproducible)? What is your sessionInfo()?

library(clusterProfiler)

data(gcSample)

xx <- compareCluster(gcSample, fun=enrichKEGG,

organism="hsa", pvalueCutoff=0.05)

xx

#

Result of Comparing 8 gene clusters

#

.. @fun enrichKEGG

.. @geneClusters List of 8

$ X1: chr [1:216] "4597" "7111" "5266" "2175" ...

$ X2: chr [1:805] "23450" "5160" "7126" "26118" ...

$ X3: chr [1:392] "894" "7057" "22906" "3339" ...

$ X4: chr [1:838] "5573" "7453" "5245" "23450" ...

$ X5: chr [1:929] "5982" "7318" "6352" "2101" ...

$ X6: chr [1:585] "5337" "9295" "4035" "811" ...

$ X7: chr [1:582] "2621" "2665" "5690" "3608" ...

$ X8: chr [1:237] "2665" "4735" "1327" "3192" ...

...Result 'data.frame': 76 obs. of 12 variables:

$ Cluster : Factor w/ 8 levels "X1","X2","X3",..: 2 2 2 3 3 3 4 4 4 4 ...

$ category : chr "Human Diseases" "Human Diseases" "Cellular Processes" "Environmental Information Processing" ...

$ subcategory: chr "Infectious disease: viral" "Immune disease" "Cell growth and death" "Signaling molecules and interaction" ...

$ ID : chr "hsa05169" "hsa05340" "hsa04110" "hsa04512" ...

$ Description: chr "Epstein-Barr virus infection" "Primary immunodeficiency" "Cell cycle" "ECM-receptor interaction" ...

$ GeneRatio : chr "23/406" "8/406" "18/406" "9/193" ...

$ BgRatio : chr "202/8662" "38/8662" "157/8662" "89/8662" ...

$ pvalue : num 6.83e-05 3.07e-04 3.83e-04 1.53e-04 3.29e-04 ...

$ p.adjust : num 0.0214 0.0399 0.0399 0.0362 0.0362 ...

$ qvalue : num 0.0199 0.0372 0.0372 0.0335 0.0335 ...

$ geneID : chr "4067/3383/7128/1869/890/1871/578/864/637/9641/6891/355/9134/5971/916/956/6850/7187/3551/919/4734/958/6772" "100/6891/3932/973/916/925/958/64421" "991/1869/890/1871/701/990/10926/9088/8317/9700/9134/1029/2810/699/11200/23594/8555/4173" "7057/3339/1299/3695/1101/3679/3910/3696/3693" ...

$ Count : int 23 8 18 9 17 19 17 10 22 19 ...

.. number of enriched terms found for each gene cluster:

.. X1: 0

.. X2: 3

.. X3: 3

.. X4: 22

.. X5: 10

.. X6: 1

.. X7: 17

.. X8: 20

#

...Citation

T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou,

W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.

The Innovation. 2021, 2(3):100141

— Reply to this email directly, view it on GitHubhttps://clicktime.symantec.com/15uBY59P1XknJ2h1XxDBg?h=3NwhEW4cTh29LHWJy6FoU6bSGd6OaiJo5FGJpbfodJA=&u=https://github.com/YuLab-SMU/clusterProfiler/issues/669%23issuecomment-1958828750, or unsubscribehttps://clicktime.symantec.com/15uBcuLfU9SNhyWw5WcLJ?h=ZtNZrpbmKFShDmL967bWnQic1Bek6T43y6v8u65cLeM=&u=https://github.com/notifications/unsubscribe-auth/BGJSULBROUYKEEI2KRHCLP3YU3U4BAVCNFSM6AAAAABDRPQ3X6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJYHAZDQNZVGA. You are receiving this because you authored the thread.Message ID: @.***>

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guidohooiveld commented 7 months ago

Happy to hear you got it somehow working, but to show for the record/archive thatcompareCluster also works with the generic function enricher:

> library(clusterProfiler)
> 
> ## load some example data
> data(gcSample)
> 
> ## manually download KEGG data; to be used as input for TERM2GENE and TERM2NAME
> kegg.data <- download_KEGG(species="hsa", keggType = "KEGG", keyType = "kegg")
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
> gene.sets <- kegg.data$KEGGPATHID2EXTID; colnames(gene.sets) <- c("PathwayID","GeneID")
> set.names <- kegg.data$KEGGPATHID2NAME; colnames(set.names) <- c("PathwayID","Description")
> 
> ## run compareCluster with generic function enricher
> yy <- compareCluster(geneClusters = gcSample,
+                      fun = "enricher",
+                      minGSSize = 10,
+                      maxGSSize = 500,
+                      pvalueCutoff = 1,
+                      pAdjustMethod = "BH",
+                      TERM2GENE = gene.sets[, c("PathwayID","GeneID") ], #proper order columns
+                      TERM2NAME = set.names[, c("PathwayID","Description") ]
+                      )
> 
> ## check
> yy
#
# Result of Comparing 8 gene clusters 
#
#.. @fun         enricher 
#.. @geneClusters       List of 8
 $ X1: chr [1:216] "4597" "7111" "5266" "2175" ...
 $ X2: chr [1:805] "23450" "5160" "7126" "26118" ...
 $ X3: chr [1:392] "894" "7057" "22906" "3339" ...
 $ X4: chr [1:838] "5573" "7453" "5245" "23450" ...
 $ X5: chr [1:929] "5982" "7318" "6352" "2101" ...
 $ X6: chr [1:585] "5337" "9295" "4035" "811" ...
 $ X7: chr [1:582] "2621" "2665" "5690" "3608" ...
 $ X8: chr [1:237] "2665" "4735" "1327" "3192" ...
#...Result      'data.frame':   226 obs. of  10 variables:
 $ Cluster    : Factor w/ 8 levels "X1","X2","X3",..: 1 1 1 2 2 2 2 2 2 2 ...
 $ ID         : chr  "hsa04061" "hsa05146" "hsa04060" "hsa05169" ...
 $ Description: chr  "Viral protein interaction with cytokine and cytokine receptor" "Amoebiasis" "Cytokine-cytokine receptor interaction" "Epstein-Barr virus infection" ...
 $ GeneRatio  : chr  "6/103" "6/103" "10/103" "23/406" ...
 $ BgRatio    : chr  "100/8661" "102/8661" "297/8661" "202/8661" ...
 $ pvalue     : num  1.18e-03 1.31e-03 2.72e-03 6.84e-05 3.08e-04 ...
 $ p.adjust   : num  0.1283 0.1283 0.1778 0.0214 0.04 ...
 $ qvalue     : num  0.1206 0.1206 0.1671 0.0199 0.0373 ...
 $ geneID     : chr  "6364/3559/2921/8793/3576/6374" "7850/2921/6317/3576/1281/22798" "7850/653/6364/3559/3595/2921/8793/10663/3576/6374" "4067/3383/7128/1869/890/1871/578/864/637/9641/6891/355/9134/5971/916/956/6850/7187/3551/919/4734/958/6772" ...
 $ Count      : int  6 6 10 23 8 18 22 13 12 14 ...
#.. number of enriched terms found for each gene cluster:
#..   X1: 3 
#..   X2: 20 
#..   X3: 5 
#..   X4: 76 
#..   X5: 48 
#..   X6: 4 
#..   X7: 36 
#..   X8: 34 
#
#...Citation
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, 
W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. 
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. 
The Innovation. 2021, 2(3):100141 

>

gongxin8888 commented 7 months ago

Thanks very much, Guido.

From: Guido Hooiveld @.> Date: Friday, February 23, 2024 at 3:27 AM To: YuLab-SMU/clusterProfiler @.> Cc: Yu, Gongxin @.>, Author @.> Subject: [EXTERNAL] [MARKETING] Re: [YuLab-SMU/clusterProfiler] problem in run compareCluster (Issue #669)

Happy to hear you got it somehow working, but to show for the record/archive that compareCluster also works with the generic function enricher:

library(clusterProfiler)

load some example data

data(gcSample)

manually download KEGG data; to be used as input for TERM2GENE and TERM2NAME

kegg.data <- download_KEGG(species="hsa", keggType = "KEGG", keyType = "kegg")

Reading KEGG annotation online: "https://clicktime.symantec.com/15tpP1jeVTHfBythNbPJs?h=BvATC_yQZMgUbXgJSVTTYf9I6zuqB-DfSvLHI1bdQ9Q=&u=https://rest.kegg.jp/link/hsa/pathway"...

Reading KEGG annotation online: "https://clicktime.symantec.com/15tpTqvvx4yFbvicv9nTV?h=gyLsJHDvW1i_tvMDv-e_jIqbdEUXLf48ayKIJRXZzyA=&u=https://rest.kegg.jp/list/pathway/hsa"...

gene.sets <- kegg.data$KEGGPATHID2EXTID; colnames(gene.sets) <- c("PathwayID","GeneID")

set.names <- kegg.data$KEGGPATHID2NAME; colnames(set.names) <- c("PathwayID","Description")

run compareCluster with generic function enricher

yy <- compareCluster(geneClusters = gcSample,

fun = "enricher",
minGSSize = 10,
maxGSSize = 500,
pvalueCutoff = 1,
pAdjustMethod = "BH",
TERM2GENE = gene.sets[, c("PathwayID","GeneID") ], #proper order columns
TERM2NAME = set.names[, c("PathwayID","Description") ]
)

check

yy

#

Result of Comparing 8 gene clusters

#

.. @fun enricher

.. @geneClusters List of 8

$ X1: chr [1:216] "4597" "7111" "5266" "2175" ...

$ X2: chr [1:805] "23450" "5160" "7126" "26118" ...

$ X3: chr [1:392] "894" "7057" "22906" "3339" ...

$ X4: chr [1:838] "5573" "7453" "5245" "23450" ...

$ X5: chr [1:929] "5982" "7318" "6352" "2101" ...

$ X6: chr [1:585] "5337" "9295" "4035" "811" ...

$ X7: chr [1:582] "2621" "2665" "5690" "3608" ...

$ X8: chr [1:237] "2665" "4735" "1327" "3192" ...

...Result 'data.frame': 226 obs. of 10 variables:

$ Cluster : Factor w/ 8 levels "X1","X2","X3",..: 1 1 1 2 2 2 2 2 2 2 ...

$ ID : chr "hsa04061" "hsa05146" "hsa04060" "hsa05169" ...

$ Description: chr "Viral protein interaction with cytokine and cytokine receptor" "Amoebiasis" "Cytokine-cytokine receptor interaction" "Epstein-Barr virus infection" ...

$ GeneRatio : chr "6/103" "6/103" "10/103" "23/406" ...

$ BgRatio : chr "100/8661" "102/8661" "297/8661" "202/8661" ...

$ pvalue : num 1.18e-03 1.31e-03 2.72e-03 6.84e-05 3.08e-04 ...

$ p.adjust : num 0.1283 0.1283 0.1778 0.0214 0.04 ...

$ qvalue : num 0.1206 0.1206 0.1671 0.0199 0.0373 ...

$ geneID : chr "6364/3559/2921/8793/3576/6374" "7850/2921/6317/3576/1281/22798" "7850/653/6364/3559/3595/2921/8793/10663/3576/6374" "4067/3383/7128/1869/890/1871/578/864/637/9641/6891/355/9134/5971/916/956/6850/7187/3551/919/4734/958/6772" ...

$ Count : int 6 6 10 23 8 18 22 13 12 14 ...

.. number of enriched terms found for each gene cluster:

.. X1: 3

.. X2: 20

.. X3: 5

.. X4: 76

.. X5: 48

.. X6: 4

.. X7: 36

.. X8: 34

#

...Citation

T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou,

W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.

The Innovation. 2021, 2(3):100141

— Reply to this email directly, view it on GitHubhttps://clicktime.symantec.com/15tpDMM5aDvUN6ErHUb1d?h=lXlIhAVFsDV9FcWoTSrRgv9GXCqfgeMLPu4llmIqe2U=&u=https://github.com/YuLab-SMU/clusterProfiler/issues/669%23issuecomment-1960910360, or unsubscribehttps://clicktime.symantec.com/15tpJBYN2qc4n34mq2zAF?h=m9VBvawBx_BfclpIE-sJEcGQvxo8jaF4n0SsOZ4ACNw=&u=https://github.com/notifications/unsubscribe-auth/BGJSULCOOYZBQGSAYTQCOJ3YVBHG3AVCNFSM6AAAAABDRPQ3X6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRQHEYTAMZWGA. You are receiving this because you authored the thread.Message ID: @.***>

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YuLab-SMU / clusterProfiler

problem in run compareCluster #669

Prerequisites

Describe your issue

Ask in the right place

Result of Comparing 8 gene clusters

.. @fun enrichKEGG

.. @geneClusters List of 8

...Result 'data.frame': 76 obs. of 12 variables:

.. number of enriched terms found for each gene cluster:

.. X1: 0

.. X2: 3

.. X3: 3

.. X4: 22

.. X5: 10

.. X6: 1

.. X7: 17

.. X8: 20

...Citation

load some example data

manually download KEGG data; to be used as input for TERM2GENE and TERM2NAME

run compareCluster with generic function enricher

check

Result of Comparing 8 gene clusters

.. @fun enricher

.. @geneClusters List of 8

...Result 'data.frame': 226 obs. of 10 variables:

.. number of enriched terms found for each gene cluster:

.. X1: 3

.. X2: 20

.. X3: 5

.. X4: 76

.. X5: 48

.. X6: 4

.. X7: 36

.. X8: 34

...Citation