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ggplot2 error: "Error in as.environment(where) : 'where' is missing"
5 messages · Bert Gunter, arun, Brian Smith +1 more
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
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.
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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