Brian Smith
2013-Jun-11 17:44 UTC
[R] ggplot2 error: "Error in as.environment(where) : 'where' is missing"
Hmm...I think it used to work before, but it gives an error now. Here is
some sample code:
============library(ggplot2)
Sample <- rep(c('A','B'),rep(10,2))
Vals <- sample(1:1000,20)
dataf <- as.data.frame(cbind(Sample,Vals))
myplot <- ggplot(dataf,aes(x=Vals,colour=Sample)) + geom_density()
myplot
============
I get the following error:
"Error in as.environment(where) : 'where' is missing"
Am I doing something wrong?
thanks!
**************** sessionInfo() ***************
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] splines grid stats graphics grDevices utils datasets
methods base
other attached packages:
[1] gridExtra_0.9.1 sm_2.2-4.1 imputation_2.0.1
locfit_1.5-9 TimeProjection_0.2.0 Matrix_1.0-12
timeDate_2160.97
[8] lubridate_1.2.0 gbm_2.0-8 survival_2.37-4
gplots_2.11.0 MASS_7.3-23 KernSmooth_2.23-10
caTools_1.14
[15] gdata_2.12.0 heatmap.plus_1.3 ggdendro_0.1-12
ggplot2_0.9.3.1 hgu133a.db_2.7.1 affy_1.34.0
genefilter_1.38.0
[22] biomaRt_2.12.0 org.Hs.eg.db_2.7.1 GOstats_2.22.0
graph_1.34.0 Category_2.22.0 GO.db_2.7.1
RSQLite_0.11.2
[29] DBI_0.2-5 geneplotter_1.34.0 lattice_0.20-15
annotate_1.34.1 AnnotationDbi_1.18.4 Biobase_2.16.0
BiocGenerics_0.2.0
[36] colorRamps_2.3 RColorBrewer_1.0-5 sparcl_1.0.3
gap_1.1-9 plotrix_3.4-6 som_0.3-5
pvclust_1.2-2
[43] RobustRankAggreg_1.0 impute_1.30.0 reshape_0.8.4
plyr_1.8 zoo_1.7-9 data.table_1.8.8
foreach_1.4.0
[50] foreign_0.8-53 languageR_1.4 preprocessCore_1.18.0
gtools_2.7.1 BiocInstaller_1.4.9 hash_2.2.6
loaded via a namespace (and not attached):
[1] affyio_1.24.0 bitops_1.0-4.2 codetools_0.2-8 colorspace_1.2-1
dichromat_2.0-0 digest_0.6.3 GSEABase_1.18.0 gtable_0.1.2
IRanges_1.14.4
[10] iterators_1.0.6 labeling_0.1 munsell_0.4 proto_0.3-10
RBGL_1.32.1 RCurl_1.95-4.1 reshape2_1.2.2 scales_0.2.3
stats4_2.15.2
[19] stringr_0.6.2 tools_2.15.2 tree_1.0-33 XML_3.96-1.1
xtable_1.7-1 zlibbioc_1.2.0
[[alternative HTML version deleted]]
Bert Gunter
2013-Jun-11 18:06 UTC
[R] ggplot2 error: "Error in as.environment(where) : 'where' is missing"
I just wanted to point out that the construction: dataf <- as.data.frame(cbind(Sample,Vals)) is **EVIL** . Why? cbind() constructs a matrix out of the separate vectors, and must coerce columns of different types, as is the case here, to do so (a matrix must be of one data type). Consequently> sapply(dataf,class)Sample Vals "factor" "factor" ## is almost certainly not what is wanted. The correct way to create the data frame is simply:> df <- data.frame(Sample, Vals) > sapply(df, class)Sample Vals "factor" "integer" I have no idea whether the evil construction this is related to your difficulties, but it couldn't help. Cheers, Bert On Tue, Jun 11, 2013 at 10:44 AM, Brian Smith <bsmith030465 at gmail.com> wrote:> Hmm...I think it used to work before, but it gives an error now. Here is > some sample code: > > ============> library(ggplot2) > Sample <- rep(c('A','B'),rep(10,2)) > Vals <- sample(1:1000,20) > dataf <- as.data.frame(cbind(Sample,Vals)) > myplot <- ggplot(dataf,aes(x=Vals,colour=Sample)) + geom_density() > myplot > ============> > I get the following error: > > "Error in as.environment(where) : 'where' is missing" > > Am I doing something wrong? > > thanks! > > > > **************** sessionInfo() *************** > > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] splines grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] gridExtra_0.9.1 sm_2.2-4.1 imputation_2.0.1 > locfit_1.5-9 TimeProjection_0.2.0 Matrix_1.0-12 > timeDate_2160.97 > [8] lubridate_1.2.0 gbm_2.0-8 survival_2.37-4 > gplots_2.11.0 MASS_7.3-23 KernSmooth_2.23-10 > caTools_1.14 > [15] gdata_2.12.0 heatmap.plus_1.3 ggdendro_0.1-12 > ggplot2_0.9.3.1 hgu133a.db_2.7.1 affy_1.34.0 > genefilter_1.38.0 > [22] biomaRt_2.12.0 org.Hs.eg.db_2.7.1 GOstats_2.22.0 > graph_1.34.0 Category_2.22.0 GO.db_2.7.1 > RSQLite_0.11.2 > [29] DBI_0.2-5 geneplotter_1.34.0 lattice_0.20-15 > annotate_1.34.1 AnnotationDbi_1.18.4 Biobase_2.16.0 > BiocGenerics_0.2.0 > [36] colorRamps_2.3 RColorBrewer_1.0-5 sparcl_1.0.3 > gap_1.1-9 plotrix_3.4-6 som_0.3-5 > pvclust_1.2-2 > [43] RobustRankAggreg_1.0 impute_1.30.0 reshape_0.8.4 > plyr_1.8 zoo_1.7-9 data.table_1.8.8 > foreach_1.4.0 > [50] foreign_0.8-53 languageR_1.4 preprocessCore_1.18.0 > gtools_2.7.1 BiocInstaller_1.4.9 hash_2.2.6 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 bitops_1.0-4.2 codetools_0.2-8 colorspace_1.2-1 > dichromat_2.0-0 digest_0.6.3 GSEABase_1.18.0 gtable_0.1.2 > IRanges_1.14.4 > [10] iterators_1.0.6 labeling_0.1 munsell_0.4 proto_0.3-10 > RBGL_1.32.1 RCurl_1.95-4.1 reshape2_1.2.2 scales_0.2.3 > stats4_2.15.2 > [19] stringr_0.6.2 tools_2.15.2 tree_1.0-33 XML_3.96-1.1 > xtable_1.7-1 zlibbioc_1.2.0 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
arun
2013-Jun-11 18:26 UTC
[R] ggplot2 error: "Error in as.environment(where) : 'where' is missing"
Hi,
dataf <- as.data.frame(cbind(Sample,Vals))
?str(dataf)
#'data.frame':??? 20 obs. of? 2 variables:
# $ Sample: Factor w/ 2 levels "A","B": 1 1 1 1 1 1 1 1 1 1
...
# $ Vals? : Factor w/ 20 levels
"121","154","159",..: 20 12 13 1 2 14 18 5 17 10
...
ggplot(dataf,aes(x=Vals,colour=Sample))+geom_density()
#Error in as.environment(where) : 'where' is missing
dataf<- data.frame(Sample,Vals)
?str(dataf)
#'data.frame':??? 20 obs. of? 2 variables:
# $ Sample: Factor w/ 2 levels "A","B": 1 1 1 1 1 1 1 1 1 1
...
# $ Vals? : int? 96 712 765 121 154 78 821 258 812 51 ...
ggplot(dataf,aes(x=Vals,colour=Sample))+geom_density() #no error
A.K.
----- Original Message -----
From: Brian Smith <bsmith030465 at gmail.com>
To: r-help Help <r-help at r-project.org>
Cc:
Sent: Tuesday, June 11, 2013 1:44 PM
Subject: [R] ggplot2 error: "Error in as.environment(where) :
'where' is
missing"
Hmm...I think it used to work before, but it gives an error now. Here is
some sample code:
============library(ggplot2)
Sample <- rep(c('A','B'),rep(10,2))
Vals <- sample(1:1000,20)
dataf <- as.data.frame(cbind(Sample,Vals))
myplot <- ggplot(dataf,aes(x=Vals,colour=Sample)) + geom_density()
myplot
============
I get the following error:
"Error in as.environment(where) : 'where' is missing"
Am I doing something wrong?
thanks!
**************** sessionInfo() ***************
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] splines? grid? ? ? stats? ? graphics? grDevices utils? ? datasets
methods? base
other attached packages:
[1] gridExtra_0.9.1? ? ? sm_2.2-4.1? ? ? ? ? ? imputation_2.0.1
locfit_1.5-9? ? ? ? ? TimeProjection_0.2.0? Matrix_1.0-12
timeDate_2160.97
[8] lubridate_1.2.0? ? ? gbm_2.0-8? ? ? ? ? ? survival_2.37-4
gplots_2.11.0? ? ? ? MASS_7.3-23? ? ? ? ? KernSmooth_2.23-10
caTools_1.14
[15] gdata_2.12.0? ? ? ? ? heatmap.plus_1.3? ? ? ggdendro_0.1-12
ggplot2_0.9.3.1? ? ? hgu133a.db_2.7.1? ? ? affy_1.34.0
genefilter_1.38.0
[22] biomaRt_2.12.0? ? ? ? org.Hs.eg.db_2.7.1? ? GOstats_2.22.0
graph_1.34.0? ? ? ? ? Category_2.22.0? ? ? GO.db_2.7.1
RSQLite_0.11.2
[29] DBI_0.2-5? ? ? ? ? ? geneplotter_1.34.0? ? lattice_0.20-15
annotate_1.34.1? ? ? AnnotationDbi_1.18.4? Biobase_2.16.0
BiocGenerics_0.2.0
[36] colorRamps_2.3? ? ? ? RColorBrewer_1.0-5? ? sparcl_1.0.3
gap_1.1-9? ? ? ? ? ? plotrix_3.4-6? ? ? ? som_0.3-5
pvclust_1.2-2
[43] RobustRankAggreg_1.0? impute_1.30.0? ? ? ? reshape_0.8.4
plyr_1.8? ? ? ? ? ? ? zoo_1.7-9? ? ? ? ? ? data.table_1.8.8
foreach_1.4.0
[50] foreign_0.8-53? ? ? ? languageR_1.4? ? ? ? preprocessCore_1.18.0
gtools_2.7.1? ? ? ? ? BiocInstaller_1.4.9? hash_2.2.6
loaded via a namespace (and not attached):
[1] affyio_1.24.0? ? bitops_1.0-4.2? codetools_0.2-8? colorspace_1.2-1
dichromat_2.0-0? digest_0.6.3? ? GSEABase_1.18.0? gtable_0.1.2
IRanges_1.14.4
[10] iterators_1.0.6? labeling_0.1? ? munsell_0.4? ? ? proto_0.3-10
RBGL_1.32.1? ? ? RCurl_1.95-4.1? reshape2_1.2.2? scales_0.2.3
stats4_2.15.2
[19] stringr_0.6.2? ? tools_2.15.2? ? tree_1.0-33? ? ? XML_3.96-1.1
xtable_1.7-1? ? zlibbioc_1.2.0
??? [[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius
2013-Jun-11 20:45 UTC
[R] ggplot2 error: "Error in as.environment(where) : 'where' is missing"
On Jun 11, 2013, at 10:44 AM, Brian Smith wrote:> Hmm...I think it used to work before, but it gives an error now. Here is > some sample code: > > ============> library(ggplot2) > Sample <- rep(c('A','B'),rep(10,2)) > Vals <- sample(1:1000,20) > dataf <- as.data.frame(cbind(Sample,Vals))It's _almost_always_ incorrect to do: as.data.frame(cbind(anything)) No error with: dataf <- data.frame(Sample,Vals)> myplot <- ggplot(dataf,aes(x=Vals,colour=Sample)) + geom_density() > myplot > ============> > I get the following error: > > "Error in as.environment(where) : 'where' is missing" > > Am I doing something wrong? > > thanks! > > > > **************** sessionInfo() *************** > > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] splines grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] gridExtra_0.9.1 sm_2.2-4.1 imputation_2.0.1 > locfit_1.5-9 TimeProjection_0.2.0 Matrix_1.0-12 > timeDate_2160.97 > [8] lubridate_1.2.0 gbm_2.0-8 survival_2.37-4 > gplots_2.11.0 MASS_7.3-23 KernSmooth_2.23-10 > caTools_1.14 > [15] gdata_2.12.0 heatmap.plus_1.3 ggdendro_0.1-12 > ggplot2_0.9.3.1 hgu133a.db_2.7.1 affy_1.34.0 > genefilter_1.38.0 > [22] biomaRt_2.12.0 org.Hs.eg.db_2.7.1 GOstats_2.22.0 > graph_1.34.0 Category_2.22.0 GO.db_2.7.1 > RSQLite_0.11.2 > [29] DBI_0.2-5 geneplotter_1.34.0 lattice_0.20-15 > annotate_1.34.1 AnnotationDbi_1.18.4 Biobase_2.16.0 > BiocGenerics_0.2.0 > [36] colorRamps_2.3 RColorBrewer_1.0-5 sparcl_1.0.3 > gap_1.1-9 plotrix_3.4-6 som_0.3-5 > pvclust_1.2-2 > [43] RobustRankAggreg_1.0 impute_1.30.0 reshape_0.8.4 > plyr_1.8 zoo_1.7-9 data.table_1.8.8 > foreach_1.4.0 > [50] foreign_0.8-53 languageR_1.4 preprocessCore_1.18.0 > gtools_2.7.1 BiocInstaller_1.4.9 hash_2.2.6 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 bitops_1.0-4.2 codetools_0.2-8 colorspace_1.2-1 > dichromat_2.0-0 digest_0.6.3 GSEABase_1.18.0 gtable_0.1.2 > IRanges_1.14.4 > [10] iterators_1.0.6 labeling_0.1 munsell_0.4 proto_0.3-10 > RBGL_1.32.1 RCurl_1.95-4.1 reshape2_1.2.2 scales_0.2.3 > stats4_2.15.2 > [19] stringr_0.6.2 tools_2.15.2 tree_1.0-33 XML_3.96-1.1 > xtable_1.7-1 zlibbioc_1.2.0 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.David Winsemius Alameda, CA, USA