ggplot2 functions not inheriting?
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Entering edit mode
@andrewjskelton73-7074
Last seen 2.0 years ago
United Kingdom

Hi, 

After updating to ggplot2 2.0 some of my visualisation code broke and in trying to figure out why, this behaviour concerned me. Running an internal ggplot2 function such as geom_point after the base call of ggplot(), it appears as if geom_point doesn't inherit the data structures from the original ggplot() call. 

Example:

test <- data.frame(a = 1:100, b = 801:900)
ggplot(test, aes(x=a, y=b)) + geom_point()
Error: geom_point requires the following missing aesthetics: x, y

Is this explicit defining of aesthetics in each internal ggplot2 call now the default behaviour? 

session info:

R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets 
 [9] methods   base     

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [2] biomaRt_2.26.1                                    
 [3] GenomicFeatures_1.22.7                            
 [4] AnnotationDbi_1.32.3                              
 [5] biovizBase_1.18.0                                 
 [6] ggbio_1.18.1                                      
 [7] cowplot_0.6.0                                     
 [8] gridExtra_2.0.0                                   
 [9] doParallel_1.0.10                                 
[10] IlluminaHumanMethylation450kmanifest_0.4.0        
[11] scales_0.3.0                                      
[12] reshape2_1.4.1                                    
[13] ggplot2_2.0.0                                     
[14] limma_3.26.4                                      
[15] lumi_2.22.0                                       
[16] minfi_1.16.0                                      
[17] bumphunter_1.10.0                                 
[18] locfit_1.5-9.1                                    
[19] iterators_1.0.8                                   
[20] foreach_1.4.3                                     
[21] Biostrings_2.38.3                                 
[22] XVector_0.10.0                                    
[23] SummarizedExperiment_1.0.2                        
[24] GenomicRanges_1.22.3                              
[25] GenomeInfoDb_1.6.1                                
[26] IRanges_2.4.6                                     
[27] S4Vectors_0.8.7                                   
[28] lattice_0.20-33                                   
[29] Biobase_2.30.0                                    
[30] BiocGenerics_0.16.1                               

loaded via a namespace (and not attached):
 [1] nlme_3.1-122             bitops_1.0-6             matrixStats_0.50.1      
 [4] RColorBrewer_1.1-2       tools_3.2.3              doRNG_1.6               
 [7] nor1mix_1.2-1            affyio_1.40.0            rpart_4.1-10            
[10] KernSmooth_2.23-15       Hmisc_3.17-1             DBI_0.3.1               
[13] mgcv_1.8-10              colorspace_1.2-6         nnet_7.3-11             
[16] methylumi_2.16.0         GGally_1.0.0             base64_1.1              
[19] preprocessCore_1.32.0    graph_1.48.0             pkgmaker_0.22           
[22] labeling_0.3             rtracklayer_1.30.1       genefilter_1.52.0       
[25] quadprog_1.5-5           affy_1.48.0              RBGL_1.46.0             
[28] stringr_1.0.0            digest_0.6.8             Rsamtools_1.22.0        
[31] foreign_0.8-66           illuminaio_0.12.0        siggenes_1.44.0         
[34] GEOquery_2.36.0          dichromat_2.0-0          BSgenome_1.38.0         
[37] RSQLite_1.0.0            BiocInstaller_1.20.1     mclust_5.1              
[40] BiocParallel_1.4.3       acepack_1.3-3.3          VariantAnnotation_1.16.4
[43] RCurl_1.95-4.7           magrittr_1.5             Formula_1.2-1           
[46] futile.logger_1.4.1      Matrix_1.2-3             Rcpp_0.12.2             
[49] munsell_0.4.2            stringi_1.0-1            nleqslv_2.9.1           
[52] MASS_7.3-45              zlibbioc_1.16.0          plyr_1.8.3              
[55] splines_3.2.3            multtest_2.26.0          annotate_1.48.0         
[58] beanplot_1.2             igraph_1.0.1             rngtools_1.2.4          
[61] corpcor_1.6.8            codetools_0.2-14         mixOmics_5.2.0          
[64] futile.options_1.0.0     XML_3.98-1.3             latticeExtra_0.6-26     
[67] lambda.r_1.1.7           gtable_0.1.2             reshape_0.8.5           
[70] xtable_1.8-0             survival_2.38-3          OrganismDbi_1.12.1      
[73] GenomicAlignments_1.6.3  registry_0.3             ellipse_0.3-8           
[76] cluster_2.0.3            rgl_0.95.1441  

Edit: Sorry, I forgot ggplot2 is in CRAN, not Bioconductor!

Edit2: Cross Posted Here for those interested

ggplot2 • 1.3k views
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1
Entering edit mode
@andrewjskelton73-7074
Last seen 2.0 years ago
United Kingdom

It seems as if a library wasn't playing well with ggplot2 and masked some key elements. 

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