Question: ggplot2 functions not inheriting?
0
gravatar for andrew.j.skelton73
3.9 years ago by
United Kingdom
andrew.j.skelton73320 wrote:

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 • 846 views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by andrew.j.skelton73320
Answer: ggplot2 functions not inheriting?
1
gravatar for andrew.j.skelton73
3.9 years ago by
United Kingdom
andrew.j.skelton73320 wrote:

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

ADD COMMENTlink written 3.9 years ago by andrew.j.skelton73320
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