nodeRenderInfo fill property not working with graph/Rgraphviz
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@cristobal-fresno-rodriguez-3838
Last seen 5.4 years ago
Argentina/Cordoba/Universidad Católica …
library(graph) library(Rgraphviz) g <- randomGraph(letters[1:4], 1:3, p=0.8) nodeRenderInfo(g) <- list(fill=c("a"="red", "b"="green")) renderGraph(layoutGraph(g)) Rgraphviz_2.2.1 graph_1.36.1 Dear list, I have upgraded Rgraphviz and graph package but, I cannot make fill property of nodeRenderInfo get to work as in previous versions. In addition the example on nodeRenderInfo does not work too. library(graph) library(Rgraphviz) g <- randomGraph(letters[1:4], 1:3, p=0.8) nodeRenderInfo(g) <- list(fill=c("a"="red", "b"="green")) renderGraph(layoutGraph(g)) plot(g) The plotted graph using renderGraph or plot function should have a and b node in red and green respectively. Instead they both are plotted in white fill color. I would appreciate any help. Thanks, Kachelo sessionInfo() R version 2.15.1 (2012-06-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=es_AR.UTF-8 LC_NUMERIC=C [3] LC_TIME=es_AR.UTF-8 LC_COLLATE=es_AR.UTF-8 [5] LC_MONETARY=es_AR.UTF-8 LC_MESSAGES=es_AR.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rgraphviz_2.2.1 graph_1.36.1 loaded via a namespace (and not attached): [1] BiocGenerics_0.4.0 stats4_2.15.1 tools_2.15.1 [[alternative HTML version deleted]]
graph Rgraphviz graph Rgraphviz • 927 views
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@kasper-daniel-hansen-2979
Last seen 11 weeks ago
United States
Hi Christobal Thanks for the bug report. I will see if I can fix this later this week. But for now, I can help by saying that it will work if you set the 'attribute' on the graph after layout. Like la <- layoutGraph(g) nodeRenderInfo(la) <- list(fill=c("a"="red", "b"="green")) renderGraph(la) This may be true for other 'attributes' as well. As an aside, there are clearly things that need to change in the entire layout/rendering process, and it is on my todo list to overhaul this system to something more streamlined. It is not really ideal that we have two different plotting systems (layoutGraph + renderGraph vs graphLayout + plot). Kasper On Tue, Nov 13, 2012 at 9:06 AM, Cristobal Fresno Rodr?guez <cristobalfresno at="" gmail.com=""> wrote: > library(graph) > library(Rgraphviz) > > g <- randomGraph(letters[1:4], 1:3, p=0.8) > nodeRenderInfo(g) <- list(fill=c("a"="red", "b"="green")) > renderGraph(layoutGraph(g)) > > Rgraphviz_2.2.1 graph_1.36.1 > > Dear list, > > I have upgraded Rgraphviz and graph package but, I cannot make fill > property of nodeRenderInfo get to work as in previous versions. In addition > the example on nodeRenderInfo does not work too. > > library(graph) > library(Rgraphviz) > > g <- randomGraph(letters[1:4], 1:3, p=0.8) > nodeRenderInfo(g) <- list(fill=c("a"="red", "b"="green")) > renderGraph(layoutGraph(g)) > plot(g) > > The plotted graph using renderGraph or plot function should have a and b > node in red and green respectively. Instead they both are plotted in white > fill color. > I would appreciate any help. > Thanks, > > Kachelo > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=es_AR.UTF-8 LC_NUMERIC=C > [3] LC_TIME=es_AR.UTF-8 LC_COLLATE=es_AR.UTF-8 > [5] LC_MONETARY=es_AR.UTF-8 LC_MESSAGES=es_AR.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Rgraphviz_2.2.1 graph_1.36.1 > > loaded via a namespace (and not attached): > [1] BiocGenerics_0.4.0 stats4_2.15.1 tools_2.15.1 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Kasper, Thanks for the workaround. Best regards, Cristobal 2012/11/13 Kasper Daniel Hansen <kasperdanielhansen@gmail.com> > Hi Christobal > > Thanks for the bug report. I will see if I can fix this later this week. > > But for now, I can help by saying that it will work if you set the > 'attribute' on the graph after layout. Like > > la <- layoutGraph(g) > nodeRenderInfo(la) <- list(fill=c("a"="red", "b"="green")) > renderGraph(la) > > This may be true for other 'attributes' as well. > > As an aside, there are clearly things that need to change in the > entire layout/rendering process, and it is on my todo list to overhaul > this system to something more streamlined. It is not really ideal > that we have two different plotting systems (layoutGraph + renderGraph > vs graphLayout + plot). > > Kasper > > On Tue, Nov 13, 2012 at 9:06 AM, Cristobal Fresno Rodríguez > <cristobalfresno@gmail.com> wrote: > > library(graph) > > library(Rgraphviz) > > > > g <- randomGraph(letters[1:4], 1:3, p=0.8) > > nodeRenderInfo(g) <- list(fill=c("a"="red", "b"="green")) > > renderGraph(layoutGraph(g)) > > > > Rgraphviz_2.2.1 graph_1.36.1 > > > > Dear list, > > > > I have upgraded Rgraphviz and graph package but, I cannot make fill > > property of nodeRenderInfo get to work as in previous versions. In > addition > > the example on nodeRenderInfo does not work too. > > > > library(graph) > > library(Rgraphviz) > > > > g <- randomGraph(letters[1:4], 1:3, p=0.8) > > nodeRenderInfo(g) <- list(fill=c("a"="red", "b"="green")) > > renderGraph(layoutGraph(g)) > > plot(g) > > > > The plotted graph using renderGraph or plot function should have a and b > > node in red and green respectively. Instead they both are plotted in > white > > fill color. > > I would appreciate any help. > > Thanks, > > > > Kachelo > > > > sessionInfo() > > R version 2.15.1 (2012-06-22) > > Platform: i686-pc-linux-gnu (32-bit) > > > > locale: > > [1] LC_CTYPE=es_AR.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=es_AR.UTF-8 LC_COLLATE=es_AR.UTF-8 > > [5] LC_MONETARY=es_AR.UTF-8 LC_MESSAGES=es_AR.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] Rgraphviz_2.2.1 graph_1.36.1 > > > > loaded via a namespace (and not attached): > > [1] BiocGenerics_0.4.0 stats4_2.15.1 tools_2.15.1 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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