WCGNA to Cytoscape
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9 months ago

Hello, im new in RNA-Seq World, and im trying to export a network from WCGNA to Cytoscape, im trying this command (and the output is here too)

> library(WGCNA);
> library(cluster);
> options(stringsAsFactors = FALSE);
> load("modulePreservation.RData");
> ADJ1=abs(cor(datExprhigado,use="p"))^6;
> lnames = load(file = "modulePreservation.RData");
> lnames;
[1] "mp"
> TOM = TOMsimilarityFromExpr(datExprhigado, power = 18);
TOM calculation: adjacency..
..will use 4 parallel threads.
 Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> annot = read.csv(file = "anotacionEG.csv");
> modules = c("turquoise", "brown");
> probes = names(datExprhigado);
> inModule = is.finite(match(moduleColorsAutomatic, modules));
> modProbes = probes[inModule];
> modGenes = annot$gene_symbol[match(modProbes, annot$substanceBXH)];
> modTOM = TOM[inModule, inModule];
> dimnames(modTOM) = list(modProbes, modProbes);> library(WGCNA);
> library(cluster);
> options(stringsAsFactors = FALSE);
> load("modulePreservation.RData");
> ADJ1=abs(cor(datExprhigado,use="p"))^6;
> lnames = load(file = "modulePreservation.RData");
> lnames;
[1] "mp"
> TOM = TOMsimilarityFromExpr(datExprhigado, power = 18);
TOM calculation: adjacency..
..will use 4 parallel threads.
 Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> annot = read.csv(file = "anotacionEG.csv");
> modules = c("turquoise", "brown");
> probes = names(datExprhigado);
> inModule = is.finite(match(moduleColorsAutomatic, modules));
> modProbes = probes[inModule];
> modGenes = annot$gene_symbol[match(modProbes, annot$substanceBXH)];
> modTOM = TOM[inModule, inModule];
> dimnames(modTOM) = list(modProbes, modProbes);
> cyt = exportNetworkToCytoscape(modTOM,
+ edgeFile = paste("CytoscapeInput-edges-", paste(modules, collapse="-"), ".txt", sep=""),
+ nodeFile = paste("CytoscapeInput-nodes-", paste(modules, collapse="-"), ".txt", sep=""),
+ weighted = TRUE,
+ threshold = 0.02,
+ nodeNames = modProbes,
+ altNodeNames = modGenes,
+ nodeAttr = moduleColorsAutomatic[inModule])
Error in exportNetworkToCytoscape(modTOM, edgeFile = paste("CytoscapeInput-edges-",  : 
  Cannot determine node names: nodeNames is NULL and adjMat has no dimnames.

Its says basically that the objetc nodeNames do not have content..and the adjMat no not have dimnames. Hoy may i solve it? is there anyway to correct this? Thank you all!

wcgna cytoscape rnaseq • 379 views
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What is the output of:

str(modProbes)
str(modTOM)

Also, can you confirm that all steps prior to exportNetworkToCytoscape(...) have completed successfully (really, confirm this)?

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Thank you kevin. Here says :

str(modProbes)
 chr [1:306] "EGR_10759" "EGR_10652" "EGR_10430" "EGR_10293" "EGR_10234" ...
> str(modTOM)
 num [1:306, 1:306] 1 0.1531 0.0905 0.0385 0.0181 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:306] "EGR_10759" "EGR_10652" "EGR_10430" "EGR_10293" ...
  ..$ : chr [1:306] "EGR_10759" "EGR_10652" "EGR_10430" "EGR_10293" ...

I think the error came from another line...i will write another answer. Thankyou!

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hi everyone, i changed my script like this:

module = "black"
probes = names(datExprhigado)
annot = read.csv(file = "anotacion.csv")
TOM = TOMsimilarityFromExpr(datExprhigado, power = 18)
inModule = is.finite(match(moduleColorsHigado, module))
modProbes = probes[inModule]
modGenes = annot$Name[match(modProbes, annot$gene_symbol)]
modTOM = TOM[inModule, inModule]
dimnames(modTOM) = list(modProbes, modProbes)
cyt = exportNetworkToCytoscape(modTOM, edgeFile =
paste("CytoscapeInput-edges-", paste(module, collapse="-"),
".txt", sep=""), nodeFile = paste("CytoscapeInput-nodes-",
paste(module, collapse="-"), ".txt", sep=""), weighted =
TRUE, threshold = 0, nodeNames = modProbes, altNodeNames =
modGenes, nodeAttr = moduleColorsHigado[inModule])

Then it outputs me txt files, in both i see the column AltName says n/a, then i saw this

str(modGenes)
 NULL

so, i think the error is here

modGenes = annot$Name[match(modProbes, annot$gene_symbol)]

I have a doubt about what to write in "Name" and "gene_symbol" fields. I think that is the error.

in my dataExprhigado the head is this

gene_symbol H1.1
EGR_11327   218.445907246019
EGR_11326   234.658689424435
EGR_11324   17.0660865035952

and in the annotation file is:

0   WormBase_imported   gene    6894    7124    .   -   .   ID=gene:EgrG_002011600  Name=EgrG_002011600 biotype=protein_coding

So, to sum up, i think the error is that i do not know what do i have to type in the field Name and gene_symbol from this line:

modGenes = annot$Name[match(modProbes, annot$gene_symbol)]

Thank you again!

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Now all resolved, or ... ?

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Hi Kevin! Thank You for your help. Still not solved, because modGenes seems to be an empty file... thanks!

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Difficult for me to debug from here. What is the output of str(annot)?

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hi again Kevin, and thank you for your patiente. I will tell you what i have done now. 1st of all my annotation file, was wrong, so i changed it (in the command line says the same name that before, but it is just a "practical" way, the file now is differente). I update what i do (and tell you too what str annot says

PART I

Script of module preservation and its output: HERE

Head of higadoData

head(higadoData)
  gene_symbol       H1.1       H1.2       H1.4       H3.1       H282       H303
1   EGR_11327  218.44591  368.56225  184.88159  167.85584  221.62129  409.12805
2   EGR_11326  234.65869  371.67686  428.80913  524.41236  486.30644  350.82002
3   EGR_11324   17.06609   19.72587   41.62256   39.49549   23.10743   55.39263
4   EGR_11318 2905.50123 1716.15040 3232.03996 2436.65242 3988.13296 3286.62962
5   EGR_11315  663.87076  483.80283  479.14339  262.20618  754.14260 1433.40588
6   EGR_11313  983.85989 1006.01920 1461.62933 2749.32507 1319.22439 3939.67962

Wcgna to Cytoscape script and output

> module = "black"
> probes = names(datExprhigado)
> annot = read.csv(file = "anotacion.csv")
> TOM = TOMsimilarityFromExpr(datExprhigado, power = 18)
TOM calculation: adjacency..
..will use 4 parallel threads.
 Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> inModule = is.finite(match(moduleColorsHigado, module))
> modProbes = probes[inModule]
> modGenes = annot$Name[match(modProbes, annot$GeneID)] #this line changed, i also tried with locus_tag , but same thing.
> modTOM = TOM[inModule, inModule]
> dimnames(modTOM) = list(modProbes, modProbes)
> cyt = exportNetworkToCytoscape(modTOM, edgeFile =
+ paste("CytoscapeInput-edges-", paste(module, collapse="-"),
+ ".txt", sep=""), nodeFile = paste("CytoscapeInput-nodes-",
+ paste(module, collapse="-"), ".txt", sep=""), weighted =
+ TRUE, threshold = 0, nodeNames = modProbes, altNodeNames =
+ modGenes, nodeAttr = moduleColorsHigado[inModule])
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PART II

Head of annot (this is the annotation file that i have changed . it is a new file, not a modifed one and the source is here [https://www.ncbi.nlm.nih.gov/genome/browse/#!/proteins/10706/50662%7CEchinococcus%20granulosus/][2] )

head(annot)
  X.Name      Accession  Start   Stop Strand   GeneID Locus locus_tag
1     Un NW_020170438.1 427312 434605      - 36342241    NA EGR_06526
2     Un NW_020170438.1 468388 471018      + 36342243    NA EGR_06528
3     Un NW_020170439.1 356859 361410      + 36342288    NA EGR_06573
4     Un NW_020170439.1 362106 367883      - 36342289    NA EGR_06574
5     Un NW_020170439.1 391807 398323      + 36342292    NA EGR_06577
6     Un NW_020170439.1 412807 417032      - 36342295    NA EGR_06580
  Protein.product Length                       Protein.Name
1  XP_024349839.1    284     hypothetical protein EGR_06526
2  XP_024349841.1    142    G-protein-signaling modulator 2
3  XP_024349782.1    562 Origin recognition complex subunit
4  XP_024349783.1    292      Mitochondrial carrier protein
5  XP_024349786.1    268     hypothetical protein EGR_06577
6  XP_024349789.1     95     hypothetical protein EGR_06580
>

And finally, the str commands you asked me and its output

str(modProbes)
 chr [1:306] "EGR_10759" "EGR_10652" "EGR_10430" "EGR_10293" "EGR_10234" ...

str(modTOM)
 num [1:306, 1:306] 1 0.1531 0.0905 0.0385 0.0181 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:306] "EGR_10759" "EGR_10652" "EGR_10430" "EGR_10293" ...
  ..$ : chr [1:306] "EGR_10759" "EGR_10652" "EGR_10430" "EGR_10293" ...

str(annot)
'data.frame':   11319 obs. of  11 variables:
 $ X.Name         : chr  "Un" "Un" "Un" "Un" ...
 $ Accession      : chr  "NW_020170438.1" "NW_020170438.1" "NW_020170439.1" "NW_020170439.1" ...
 $ Start          : int  427312 468388 356859 362106 391807 412807 431647 448990 453081 486099 ...
 $ Stop           : int  434605 471018 361410 367883 398323 417032 432700 449131 460320 487128 ...
 $ Strand         : chr  "-" "+" "+" "-" ...
 $ GeneID         : int  36342241 36342243 36342288 36342289 36342292 36342295 36342297 36342299 36342301 36342305 ...
 $ Locus          : logi  NA NA NA NA NA NA ...
 $ locus_tag      : chr  "EGR_06526" "EGR_06528" "EGR_06573" "EGR_06574" ...
 $ Protein.product: chr  "XP_024349839.1" "XP_024349841.1" "XP_024349782.1" "XP_024349783.1" ...
 $ Length         : int  284 142 562 292 268 95 335 31 498 119 ...
 $ Protein.Name   : chr  "hypothetical protein EGR_06526" "G-protein-signaling modulator 2" "Origin recognition complex subunit" "Mitochondrial carrier protein" ...

After all of this, i may get the .txt input files to cytoscape, BUT the column fromAltName and toAltName still says N/A, as you may see in this image:

![https://ibb.co/rmvyWLb][3]

Im not really sure what is happening, i thought the problema was that when i wrote "gene_symbol" ,as in the other messages i told you, because in the annot object there is no column called like this. But i tried changing to GeneID and to locus_tag and still is the same...

Thank you for you kindly help and patience!

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No hay de que. Es aún difícil saber lo que está pasando. Pues / so, the issue is most likely here:

modGenes = annot$Name[match(modProbes, annot$GeneID)]

I think that it should be / debe ser:

modGenes = annot$X.Name[match(modProbes, annot$locus_tag)]

...oppure:

modGenes = annot$Protein.Name[match(modProbes, annot$locus_tag)]
modGenes = annot$Accession[match(modProbes, annot$locus_tag)]
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