WGCNA of RNA seq data, Error in function plotDendroAndColors
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
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just dev.off() until you get error and run your code again
Try saving the figure to file and set the dimensions with, for example:
The default width and height is just 7 inches for
pdf().You obviously have high density data.