Here is my issue: I am looping around my data. For each iteration of the loop, I create 3 plots that I organize on the same page, and I want to have one page per iteration stored in the same pdf file.
I am using ggarrange from the ggpubr package (I want plot 3 to be displayed on the second row and to span 2 columns).
Here is how I proceed (on some test data):
I create test data frames:
tt <- data.frame(group=rep(c("A", "B"), 3), value=1:6)
tt2 <- data.frame(x=1:10, y=1:10)
I create and store the plots in objects:
p1 <- ggplot(tt, aes(x=group, y=value, fill=group)) +
geom_dotplot(binaxis="y")
p2 <- ggplot(tt, aes(x=group, y=value, fill=group)) + geom_boxplot()
p3 <- ggplot(tt2, aes(x=x, y=y)) + geom_point()
This works:
pdf("test.pdf")
ggarrange(ggarrange(p1, p2),
p3,
nrow=2,
heights=c(2, 1))
dev.off()
This doesn't work (it does not throw an error but the pdf file does not contain any page):
pdf("test.pdf")
for(i in 1:2){
ggarrange(ggarrange(p1, p2),
p3,
nrow=2,
heights=c(2, 1))
}
dev.off()
I thought maybe the nested ggarrange could be an issue, but this also doesn't work:
pdf("test.pdf")
for(i in 1:2){
ggarrange(p1, p2)
}
dev.off()
I also realized that opening and closing the pdf file inside the for loop fails as well:
for(i in 1:2){
pdf(paste0("test",i,".pdf"))
ggarrange(p1, p2)
dev.off()
}
EDIT! I found that the alternative using grid.arrange from the gridExtra package works:
pdf("test.pdf")
for(i in 1:2){
grid.arrange(
p1, p2, p3,
nrow=2, ncol=2,
layout_matrix = rbind(c(1, 2),
c(3, 3))
)
}
dev.off()
But I'm still interested to know why it fails with the ggarrange code so does anyone know how to deal with this?
Thank you!
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.2 (Nitrogen)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggpubr_0.1.8 magrittr_1.5 BiocInstaller_1.30.0
[4] gtable_0.2.0 gplots_3.0.1 RColorBrewer_1.1-2
[7] scales_0.5.0 gridExtra_2.3 cowplot_0.9.2
[10] reshape2_1.4.3 ggplot2_2.2.1
loaded via a namespace (and not attached):
[1] Category_2.46.0 bitops_1.0-6
[3] matrixStats_0.53.1 bit64_0.9-7
[5] progress_1.1.2 httr_1.3.1
[7] GenomeInfoDb_1.16.0 Rgraphviz_2.24.0
[9] tools_3.5.0 backports_1.1.2
[11] R6_2.2.2 KernSmooth_2.23-15
[13] DBI_1.0.0 lazyeval_0.2.1
[15] BiocGenerics_0.26.0 colorspace_1.3-2
[17] prettyunits_1.0.2 compiler_3.5.0
[19] bit_1.1-12 sendmailR_1.2-1
[21] graph_1.58.0 Biobase_2.40.0
[23] DelayedArray_0.6.1 labeling_0.3
[25] rtracklayer_1.40.3 caTools_1.17.1
[27] checkmate_1.8.5 BatchJobs_1.7
[29] genefilter_1.62.0 RBGL_1.56.0
[31] stringr_1.3.0 digest_0.6.15
[33] Rsamtools_1.32.0 AnnotationForge_1.22.0
[35] XVector_0.20.0 base64enc_0.1-3
[37] pkgconfig_2.0.1 limma_3.36.2
[39] rlang_0.2.0 RSQLite_2.0
[41] BBmisc_1.11 bindr_0.1.1
[43] GOstats_2.46.0 hwriter_1.3.2
[45] BiocParallel_1.14.1 gtools_3.5.0
[47] dplyr_0.7.4 RCurl_1.95-4.10
[49] GO.db_3.6.0 GenomeInfoDbData_1.1.0
[51] Matrix_1.2-12 Rcpp_0.12.16
[53] munsell_0.4.3 S4Vectors_0.18.3
[55] stringi_1.1.7 edgeR_3.22.3
[57] SummarizedExperiment_1.10.1 zlibbioc_1.26.0
[59] plyr_1.8.4 blob_1.1.0
[61] ggrepel_0.8.0 parallel_3.5.0
[63] gdata_2.18.0 lattice_0.20-35
[65] Biostrings_2.48.0 splines_3.5.0
[67] GenomicFeatures_1.32.0 annotate_1.58.0
[69] locfit_1.5-9.1 pillar_1.2.1
[71] tcltk_3.5.0 GenomicRanges_1.32.3
[73] rjson_0.2.15 systemPipeR_1.14.0
[75] DiffBind_2.8.0 biomaRt_2.36.1
[77] stats4_3.5.0 glue_1.2.0
[79] XML_3.98-1.10 ShortRead_1.38.0
[81] latticeExtra_0.6-28 data.table_1.10.4-3
[83] purrr_0.2.4 amap_0.8-16
[85] assertthat_0.2.0 xtable_1.8-2
[87] survival_2.41-3 tibble_1.4.2
[89] pheatmap_1.0.8 GenomicAlignments_1.16.0
[91] AnnotationDbi_1.42.1 memoise_1.1.0
[93] IRanges_2.14.10 bindrcpp_0.2
[95] brew_1.0-6 GSEABase_1.42.0
