addEdge, edgeData and quotations

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Mark Grimes

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Apr 22, 2013, 11:22:18 PM4/22/13

to Paul Shannon, rcyto...@googlegroups.com

Paul

Something is broken that used to work. I hope this is easy to fix - and not due to a glitch introduced in R 3.0. I am using methods to load edges that were working before, and are not. The session transcript is pasted below. I tried changing to mode="character", converting to a matrix, and nothing got rid of the weird characters screwing up the edge names.

Thanks for your help,

Mark Grimes

> sessionInfo()

R version 3.0.0 (2013-04-03)

Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] parallel grid splines stats graphics grDevices utils datasets methods base

other attached packages:

[1] rgl_0.93.932 plyr_1.8 GOstats_2.26.0 Category_2.26.0 GO.db_2.9.0 org.Hs.eg.db_2.9.0

[7] RSQLite_0.11.2 DBI_0.2-5 AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0 RCytoscape_1.10.0

[13] XMLRPC_0.3-0 graph_1.38.0 gplots_2.11.0 KernSmooth_2.23-10 caTools_1.14 gdata_2.12.0

[19] gtools_2.7.1 tsne_0.1-2 vegan_2.0-7 permute_0.7-0 RUnit_0.4.26 bio3d_1.1-5

[25] adegenet_1.3-7 ape_3.0-8 igraph_0.6.5-1 ade4_1.5-2 MASS_7.3-26 cluster_1.14.4

[31] Hmisc_3.10-1 survival_2.37-4 stringr_0.6.2 fdrtool_1.2.10 qgraph_1.2.1

loaded via a namespace (and not attached):

[1] annotate_1.38.0 AnnotationForge_1.2.0 bitops_1.0-5 ellipse_0.3-7 genefilter_1.42.0 GSEABase_1.22.0

[7] IRanges_1.18.0 jpeg_0.1-2 lattice_0.20-15 lavaan_0.5-12 nlme_3.1-109 png_0.1-4

[13] psych_1.3.2 RBGL_1.36.0 RCurl_1.95-4.1 sem_3.1-3 stats4_3.0.0 tools_3.0.0

[19] XML_3.95-0.2 xtable_1.7-1

> # Send to Cytoscape

> rcyq <- new("graphNEL", edgemode='directed', nodes=as.character(nodeats$node))

> rcyq <- initNodeAttribute (graph= rcyq, attribute.name="nodeType", attribute.type='char', default.value="undefined")

> nodeData (rcyq, n=as.character(nodeats$node), attr="nodeType") <- as.character(nodeats$nodeType)

> # load standard edge attributes

> rcyq <- initEdgeAttribute (graph= rcyq, attribute.name='edgeType', attribute.type='char', default.value='undefined')

> rcyq <- initEdgeAttribute(rcyq, attribute.name = "weight", attribute.type = "numeric", default.value = 0.0)

> rcyq <- addEdge (ssed.n$from, ssed.n$to, rcyq)

Error in .local(object, from, to, ...) : unknown nodes in 'from': ‚ÄòABL1 185, 204‚Äô, ‚ÄòABL1 226, 245‚Äô, ‚ÄòABL1 257, 276‚Äô, ‚ÄòABL1 392, 411, 438, 402‚Äô, ‚ÄòABL1 393, 412, 439, 403‚Äô, ‚ÄòABL1 394, 413, 440, 404‚Äô, ‚ÄòABL2 272, 236‚Äô, ‚ÄòABL2 412‚Äô, ‚ÄòABL2 718‚Äô, ‚ÄòAXL 702‚Äô, ‚ÄòAXL 702, 703‚Äô, ‚ÄòAXL 703‚Äô, ‚ÄòBCAR3 117‚Äô, ‚ÄòBCAR3 212‚Äô, ‚ÄòBCAR3 266‚Äô, ‚ÄòCBL 674‚Äô, ‚ÄòCBL 675‚Äô, ‚ÄòCBL 700‚Äô, ‚ÄòCBL 731‚Äô, ‚ÄòCBL 767, 774‚Äô, ‚ÄòCBL 774‚Äô, ‚ÄòCBLB 665‚Äô, ‚ÄòCBLB 709‚Äô, ‚ÄòCBLB 889‚Äô, ‚ÄòCRK 221‚Äô, ‚ÄòCRK 251‚Äô, ‚ÄòCRK 41‚Äô, ‚ÄòCRKL 132‚Äô, ‚ÄòCRKL 197, 207‚Äô, ‚ÄòCRKL 198‚Äô, ‚ÄòCRKL 198, 207‚Äô, ‚ÄòCRKL 207‚Äô, ‚ÄòCRKL 251‚Äô, ‚ÄòDDR1 792, 796‚Äô, ‚ÄòDDR2 461, 471, 71, 81‚Äô, ‚ÄòDDR2 469, 79‚Äô, ‚ÄòDDR2 470, 485, 80, 95‚Äô, ‚ÄòDDR2 471, 81‚Äô, ‚ÄòDDR2 481‚Äô, ‚ÄòDDR2 481, 91‚Äô, ‚ÄòDDR2 521‚Äô, ‚ÄòDDR2 736, 740‚Äô, ‚ÄòDDR2 736, 740, 741‚Äô, ‚ÄòDDR2 740‚Äô, ‚ÄòDDR2 740, 741‚Äô, ‚ÄòEGFR 1110‚Äô, ‚ÄòEGFR 1172‚Äô, ‚ÄòEGFR 1197‚Äô, ‚ÄòEGFR 727, 735, 733‚Äô, ‚ÄòEGFR 869‚Äô, ‚ÄòEPHA2 575‚Ä

> rcyq <- addEdge (as.vector(ssed.n$from, mode="character"), as.vector(ssed.n$to, mode="character"), rcyq)

> ssed.m <- as.matrix(ssed.n)

> rcyq <- addEdge (ssed.m$from, ssed.m$to, rcyq)

Error in addEdge(ssed.m$from, ssed.m$to, rcyq) :

error in evaluating the argument 'from' in selecting a method for function 'addEdge': Error in ssed.m$from : $ operator is invalid for atomic vectors

> rcyq <- addEdge (as.vector(ssed.m[,"from"], mode="character"), as.vector(ssed.m[,"to"], mode="character"), rcyq)

> edgeData (rcyq, as.vector(ssed.n$from, mode="character"), as.vector(ssed.n$to, mode="character"), attr='edgeType') <- as.character(ssed.n$edgeType)

> edgeData (rcyq, as.vector(ssed.n$from, mode="character"), as.vector(ssed.n$to, mode="character"), attr='Weight') <-as.numeric(ssed.n$weight)

> #

> rcyq.window <- new.CytoscapeWindow ("Corr Edges", graph= rcyq)

estimated displayGraph time: 0.4 seconds

adding 92 nodes...

sending 92 nodes

ending sendNodes

adding 0 edges...

CytoscapeWindow.sendEdges, no edges in graph. returning

adding node attributes...

[1] "nodeType"

[1] "label"

adding edge attributes...

[1] "edgeType"

[1] "weight"

# This all works. Not sure what is going on with the edge names.

# Here is what the edge file looks like

> head(ssed.n) # class = data.frame

from to Weight edgeType

1 ALK 1278 ALK 1278, 1282 -1.0000000 correlation

2 ALK 1278 ALK 138 0.5000000 correlation

3 ALK 1278, 1282 ALK 138 -0.5000000 correlation

4 ALK 1096, 156 ALK 1506, 566 -0.1000000 correlation

5 ALK 1096 ALK 1507 0.2000000 correlation

6 ALK 1096, 156 ALK 1507, 567 -0.1666667 correlation

> head(ssed.m) # class = matrix

from to Weight edgeType

1 "ALK 1278" "ALK 1278, 1282" "-1.00000000" "correlation"

2 "ALK 1278" "ALK 138" " 0.50000000" "correlation"

3 "ALK 1278, 1282" "ALK 138" "-0.50000000" "correlation"

4 "ALK 1096, 156" "ALK 1506, 566" "-0.10000000" "correlation"

5 "ALK 1096" "ALK 1507" " 0.20000000" "correlation"

6 "ALK 1096, 156" "ALK 1507, 567" "-0.16666667" "correlation"

Paul Shannon

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Apr 23, 2013, 12:55:46 AM4/23/13

to Mark Grimes, Paul Shannon, rcyto...@googlegroups.com

Hi Mark,

I think those odd umlaut characters will help us to track down this bug. Somehow, for instance, ABL because A-umlaut, o-accent, ABL1.

Is it possible to whittle this down to a tiny (nano-scale) example? Something like this:

rcyq <- new("graphNEL", edgemode='directed', nodes=c("A", "B")
rcyq <- addEdge ("A", "B", rcyq)

such that you reproduce the "unknown nodes in 'from'" error?

There may have been some discussion recently about text encoding oddness in R 3.0. A minimal reproducible example of the problem is what we need!

- Paul

For instance

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