Question: WGCNA of RNA seq data, Error in function plotDendroAndColors
0
gravatar for i.elshesheny
13 months ago by
i.elshesheny0 wrote:

I am using WGCNA package in R (weighted correlation network analysis) I would like to ask about an error in R program: The ERROR:

Error in plot.new() : outer margins too large (figure region too small)

This error occurs when I run the following command:

plotDendroAndColors(geneTree, moduleColorsManual1, groupLabels=("Tree Cut"),
                    dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05,
                    main = "Gene dendrogram and module colors")

I have tried all possible solution such as:

windows()
par("mar")
par(mar=c(1,1,1,1))
par(oma=c(5,7,1,1))
par(mar = rep(2, 4))
graphics.off()
dev.off()
options(jupyter.plot_mimetypes = 'image/png')

but unfortunately I still have the same error.

If any one have any solution for this issue, it will be appreciated

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] cluster_2.0.7-1       flashClust_1.01-2     WGCNA_1.63            fastcluster_1.1.25   
[5] dynamicTreeCut_1.63-1 edgeR_3.20.9          limma_3.34.9         

loaded via a namespace (and not attached):
 [1] robust_0.4-18         Rcpp_0.12.18          locfit_1.5-9.1        mvtnorm_1.0-8        
 [5] lattice_0.20-35       GO.db_3.5.0           digest_0.6.15         foreach_1.4.4        
 [9] plyr_1.8.4            backports_1.1.2       acepack_1.4.1         pcaPP_1.9-73         
[13] stats4_3.4.3          RSQLite_2.1.1         ggplot2_3.0.0         pillar_1.3.0         
[17] rlang_0.2.2           lazyeval_0.2.1        rstudioapi_0.7        data.table_1.11.4    
[21] blob_1.1.1            S4Vectors_0.16.0      rpart_4.1-13          Matrix_1.2-14        
[25] checkmate_1.8.5       preprocessCore_1.40.0 splines_3.4.3         stringr_1.3.1        
[29] foreign_0.8-71        htmlwidgets_1.2       bit_1.1-14            munsell_0.5.0        
[33] compiler_3.4.3        pkgconfig_2.0.2       BiocGenerics_0.24.0   base64enc_0.1-3      
[37] htmltools_0.3.6       nnet_7.3-12           tibble_1.4.2          gridExtra_2.3        
[41] htmlTable_1.12        Hmisc_4.1-1           IRanges_2.12.0        codetools_0.2-15     
[45] matrixStats_0.54.0    rrcov_1.4-4           crayon_1.3.4          MASS_7.3-50          
[49] grid_3.4.3            gtable_0.2.0          DBI_1.0.0             magrittr_1.5         
[53] scales_1.0.0          stringi_1.1.7         impute_1.52.0         doParallel_1.0.11    
[57] latticeExtra_0.6-28   robustbase_0.93-2     Formula_1.2-3         RColorBrewer_1.1-2   
[61] iterators_1.0.10      tools_3.4.3           bit64_0.9-7           Biobase_2.38.0       
[65] DEoptimR_1.0-8        fit.models_0.5-14     parallel_3.4.3        survival_2.42-6      
[69] AnnotationDbi_1.40.0  colorspace_1.3-2      memoise_1.1.0         knitr_1.20
wgcna rna-seq R • 594 views
ADD COMMENTlink modified 13 months ago by Kevin Blighe48k • written 13 months ago by i.elshesheny0

just dev.off() until you get error and run your code again

ADD REPLYlink written 13 months ago by krushnach80580

Try saving the figure to file and set the dimensions with, for example:

pdf("figure.pdf", width=12, height=12)
    plotDendroAndColors(geneTree, moduleColorsManual1, groupLabels=("Tree Cut"),
                    dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05,
                    main = "Gene dendrogram and module colors")
dev.off()

The default width and height is just 7 inches for pdf().

You obviously have high density data.

ADD REPLYlink modified 13 months ago • written 13 months ago by Kevin Blighe48k
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