ViSEAGO issueshttps://forgemia.inra.fr/umr-boa/viseago/-/issues2019-12-20T13:33:28+01:00https://forgemia.inra.fr/umr-boa/viseago/-/issues/1Terms display on heatmap2019-12-20T13:33:28+01:00Boulais JonathanTerms display on heatmapHi!
Thanks for the package. Although the package seems to address the redundancy problem from GO terms, the GOterms_heatmap visual output could be greatly improved. Is there a way to display the terms name on the heatmap? Also, how do w...Hi!
Thanks for the package. Although the package seems to address the redundancy problem from GO terms, the GOterms_heatmap visual output could be greatly improved. Is there a way to display the terms name on the heatmap? Also, how do we change the heatmap colors?
Thanks !https://forgemia.inra.fr/umr-boa/viseago/-/issues/3demo file ?2020-02-25T14:32:23+01:00Carine Genetdemo file ?hi,
I was trying to reproduce the pipeline provided there https://bioconductor.org/packages/release/bioc/vignettes/ViSEAGO/inst/doc/ViSEAGO.html
BUT there is no background.txt file (instead --> background_L.txt)
And There is no selecti...hi,
I was trying to reproduce the pipeline provided there https://bioconductor.org/packages/release/bioc/vignettes/ViSEAGO/inst/doc/ViSEAGO.html
BUT there is no background.txt file (instead --> background_L.txt)
And There is no selection.txt file
Best
Carinehttps://forgemia.inra.fr/umr-boa/viseago/-/issues/4Demo file and merge_enrich_terms error2023-03-24T09:58:40+01:00Panda sayamDemo file and merge_enrich_terms errorHi,
I wanted to implement the pipeline in my research paper work but I am facing issues while using ViSEAGO::merge_enrich_terms(Input=list(condition=c("BP","elim"))) command,
it gives an - **Error in setnames(x, value) : Can't assign ...Hi,
I wanted to implement the pipeline in my research paper work but I am facing issues while using ViSEAGO::merge_enrich_terms(Input=list(condition=c("BP","elim"))) command,
it gives an - **Error in setnames(x, value) : Can't assign 3 names to a 2 column data.table**
In addition, it would be great if you can directly provide the link to demo datasets as its not available in the ViSEAGO tutorial. Thank you in advance.https://forgemia.inra.fr/umr-boa/viseago/-/issues/5Issue with fgsea merge2023-03-24T10:03:56+01:00Okondo MarianIssue with fgsea mergeI think there is an issue with the code to merge gsea results
It gives giving me the error
Error in `[.data.frame`(Data, , Id) : object 'Id' not found
I think Data[, Id] should look like this Data[, "Id"]I think there is an issue with the code to merge gsea results
It gives giving me the error
Error in `[.data.frame`(Data, , Id) : object 'Id' not found
I think Data[, Id] should look like this Data[, "Id"]https://forgemia.inra.fr/umr-boa/viseago/-/issues/6Erreur dans hm$x$data[[col]] : un tel index n'existe pas au niveau 22023-05-11T11:30:07+02:00Sebastien Theilsebastien.theil@inra.frErreur dans hm$x$data[[col]] : un tel index n'existe pas au niveau 2Bonjour,
petit "bug" que je n'arrive pas à comprendre dans la fonction `ViSEAGO::GOterms_heatmap` avec l'ontology 'CC' (fonctionne avec les autres ontologies).
Voici mon code (copier coller du tuto) :
```
Wang_clusters_wardD2 <- ViSEAG...Bonjour,
petit "bug" que je n'arrive pas à comprendre dans la fonction `ViSEAGO::GOterms_heatmap` avec l'ontology 'CC' (fonctionne avec les autres ontologies).
Voici mon code (copier coller du tuto) :
```
Wang_clusters_wardD2 <- ViSEAGO::GOterms_heatmap(
myGOs,
showIC=TRUE,
showGOlabels=TRUE,
GO.tree=list(
tree=list(
distance="Wang",
aggreg.method="ward.D2"
),
cut=list(
dynamic=list(
pamStage=TRUE,
pamRespectsDendro=TRUE,
deepSplit=2,
minClusterSize =2
)
)
),
samples.tree=NULL
)
```
Voici mon objet `myGOs`.
[myGOs.rda](/uploads/7ff2031aaffad53a960ba830ba3f11ba/myGOs.rda)
Merci pour ce super package et merci d'avance pour votre aide !
Sébastienhttps://forgemia.inra.fr/umr-boa/viseago/-/issues/7Error in download.file(paste("ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/", : ...2023-09-04T15:03:48+02:00Pierre BlavyError in download.file(paste("ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/", : the 'internal' method for ftp:// URLs is defunctBonjour
Quand on lance
```
Uniprot<-ViSEAGO::Uniprot2GO()
myGENE2GO<-ViSEAGO::annotate("Uniprot_id",Uniprot);
```
On a l'erreur
```
Error in download.file(paste("ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/", :
the 'internal' method ...Bonjour
Quand on lance
```
Uniprot<-ViSEAGO::Uniprot2GO()
myGENE2GO<-ViSEAGO::annotate("Uniprot_id",Uniprot);
```
On a l'erreur
```
Error in download.file(paste("ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/", :
the 'internal' method for ftp:// URLs is defunct
```
Le problème vient de la fonction download.file. En effet la méthode "internal" ne permet plus de télécharger les fichiers en FTP
(source : https://developer.r-project.org/blosxom.cgi/R-devel/2021/05/26 ).
FIX :
Il ne faut pas spécifier le paramètre method de download.file. Sa valeur par défaut va utiliser curl, qui contrairement à "internal" sait télécharger un fichier. De plus il y a plus de chances que les paramètres par défaut aient une valeur de méthode qui correspondent à ce qui sera maintenu dans le code futur, donc mieux vaut ne pas définir method pour download.file.
Pouvez vous mettre le code à jour?
Bonne journée!https://forgemia.inra.fr/umr-boa/viseago/-/issues/8url error for Uniprot annotate2023-12-08T10:16:39+01:00HILPERT Cecileurl error for Uniprot annotateHi,
I installed Viseago from this gitlab repository and I have an error when I try to run :
```
myGENE2GO<-ViSEAGO::annotate(
"Uniprot_id",
Uniprot
)
```
gives me this :
```
Dans download.file(paste("https://ftp.ebi.ac.uk/pub/data...Hi,
I installed Viseago from this gitlab repository and I have an error when I try to run :
```
myGENE2GO<-ViSEAGO::annotate(
"Uniprot_id",
Uniprot
)
```
gives me this :
```
Dans download.file(paste("https://ftp.ebi.ac.uk/pub/databases/GO/goa/", :
ouverture de l’URL 'https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT_ID/goa_Uniprot_id.gaf.gz' impossible : le statut HTTP était '404 Not Found'
```
I think the ebi path may be outdated ?
Thanks for your helphttps://forgemia.inra.fr/umr-boa/viseago/-/issues/9Error in ViSEAGO::EntrezGene2GO() function2024-01-12T10:00:08+01:00FRANKLIN EllisError in ViSEAGO::EntrezGene2GO() functionOne of the first steps in the ViSEAGO workflow is to access the GO annotation database of choice. In my case, I am choosing the EntrezGene database. I applied this line of code :
`EntrezGene <- ViSEAGO::EntrezGene2GO()`
Nevertheless, af...One of the first steps in the ViSEAGO workflow is to access the GO annotation database of choice. In my case, I am choosing the EntrezGene database. I applied this line of code :
`EntrezGene <- ViSEAGO::EntrezGene2GO()`
Nevertheless, after a minute I get this error :
```
Erreur dans download.file("ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz", :
impossible d'ouvrir l'URL 'ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz'
De plus : Messages d'avis :
1: Dans download.file("ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz", :
taille téléchargée 0 != taille déclarée 0
2: Dans download.file("ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz", :
URL ‘ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz’: délais maximal de 60 secondes atteint
```
I am unable to proceed with the analysis. Please can you inform if I am missing something. If not, please update the function.
Thank you in advance.