search

lawremi / ggbio

Grid and ggplot2 based visualization for biological data
111 stars 24 forks source link

Plotting of the GRanges objects not working #10

Closed nbartonicek closed 12 years ago

nbartonicek commented 12 years ago

Hi,

I was having problems with the basic functionality of plotting exons. The error (copied code from the intro.pdf) I was getting was:

library(TxDb.Hsapiens.UCSC.hg19.knownGene) data(genesymbol) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene exons.tx <- exonsBy(txdb, by = "tx") exons.rbm17 <- subsetByOverlaps(exons.tx, genesymbol["RBM17"]) nms <- names(exons.rbm17) freqs <- c(100, 200, 300) names(freqs) <- nms p.splice1 <- qplot(exons.rbm17) Error in continuous_scale("size", "size_c", rescale_pal(range), ...) : unused argument(s) (to = c(5, 17))

The sessionInfo() is below. It was 2.14.1. R as in the sessionInfo of the vignette.

Then I installed the new beta R 2.15 and the developer's ggbio. I get two messages:

  1. dataset genesymbol is missing
  2. Examples 3.3.2. and 3.4. from intro.pdf do not work - I can't perform overlap with GRanges or IRanges:

ir <- ranges(gr[seqnames(gr) == "chr1"])[1:3] p1 <- qplot(ir) + opts(title = "full") p1 Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class 'structure("IRanges", package = "IRanges")' into a data.frame

Hope this helps.

Cheers,

Nenad

sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 [2] GenomicFeatures_1.6.8
[3] AnnotationDbi_1.16.19
[4] Biobase_2.14.0
[5] BiocInstaller_1.2.1
[6] GenomicRanges_1.6.7
[7] IRanges_1.12.6
[8] ggbio_1.0.4
[9] ggplot2_0.9.0
[10] biovizBase_1.0.4

loaded via a namespace (and not attached): [1] biomaRt_2.10.0 Biostrings_2.22.0 bitops_1.0-4.1 BSgenome_1.22.0
[5] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2
[9] grid_2.14.1 gridExtra_0.9 MASS_7.3-17 memoise_0.1
[13] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [17] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.6.3 RSQLite_0.11.1
[21] rtracklayer_1.14.4 scales_0.2.0 stringr_0.6 tools_2.14.1
[25] XML_3.9-4 zlibbioc_1.0.1

sessionInfo() R version 2.15.0 beta (2012-03-20 r58793) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 [2] GenomicFeatures_1.7.33
[3] AnnotationDbi_1.17.27
[4] Biobase_2.15.4
[5] GenomicRanges_1.7.36
[6] IRanges_1.13.31
[7] BiocGenerics_0.1.14
[8] ggbio_1.1.7
[9] ggplot2_0.9.0
[10] devtools_0.6
[11] BiocInstaller_1.3.7

loaded via a namespace (and not attached): [1] biomaRt_2.11.2 Biostrings_2.23.6 biovizBase_1.1.12 bitops_1.0-4.1
[5] BSgenome_1.23.4 cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5
[9] dichromat_1.2-4 digest_0.5.2 grid_2.15.0 gridExtra_0.9
[13] Hmisc_3.9-2 lattice_0.20-6 MASS_7.3-17 memoise_0.1
[17] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [21] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.7.40 RSQLite_0.11.1
[25] rtracklayer_1.15.7 scales_0.2.0 stats4_2.15.0 stringr_0.6
[29] tcltk_2.15.0 tools_2.15.0 XML_3.9-4 zlibbioc_1.1.1

nbartonicek commented 12 years ago

The problem was that the tutorial examples did not work, but the real life one do.

Thanks,

Nenad

tengfei commented 12 years ago

Hi Nenad,

Thanks for reporting this issue, sorry that in the new ggbio, "qplot" will be dropped, and new "autoplot" will be the new generic function, that is based on recent ggplot2 udpate(0.9 have a autoplot generic function).

please get back later after this Friday(which is deadline for release for bioc 2.10), most part of the old vignette(in the intro.pdf) would be gone, please check the website later

http://tengfei.github.com/ggbio

I currently only updated the geom part in tutorial, by friday, most part in tutorial will be updated. So in the future, I will put documentation tutorial on-line.

I will get back to this issue on Friday and give you a new example for that.

Thanks

Tengfei

On Wed, Mar 21, 2012 at 7:21 AM, nbartonicek < reply@reply.github.com

wrote:

Hi,

I was having problems with the basic functionality of plotting exons. The error (copied code from the intro.pdf) I was getting was:

library(TxDb.Hsapiens.UCSC.hg19.knownGene) data(genesymbol) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene exons.tx <- exonsBy(txdb, by = "tx") exons.rbm17 <- subsetByOverlaps(exons.tx, genesymbol["RBM17"]) nms <- names(exons.rbm17) freqs <- c(100, 200, 300) names(freqs) <- nms p.splice1 <- qplot(exons.rbm17) Error in continuous_scale("size", "size_c", rescale_pal(range), ...) : unused argument(s) (to = c(5, 17))

The sessionInfo() is below. It was 2.14.1. R as in the sessionInfo of the vignette.

Then I installed the new beta R 2.15 and the developer's ggbio. I get two messages:

  1. dataset genesymbol is missing
  2. Examples 3.3.2. and 3.4. from intro.pdf do not work - I can't perform overlap with GRanges or IRanges:

ir <- ranges(gr[seqnames(gr) == "chr1"])[1:3] p1 <- qplot(ir) + opts(title = "full") p1 Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class 'structure("IRanges", package = "IRanges")' into a data.frame

Hope this helps.

Cheers,

Nenad

sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 [2] GenomicFeatures_1.6.8 [3] AnnotationDbi_1.16.19 [4] Biobase_2.14.0 [5] BiocInstaller_1.2.1 [6] GenomicRanges_1.6.7 [7] IRanges_1.12.6 [8] ggbio_1.0.4 [9] ggplot2_0.9.0 [10] biovizBase_1.0.4

loaded via a namespace (and not attached): [1] biomaRt_2.10.0 Biostrings_2.22.0 bitops_1.0-4.1 BSgenome_1.22.0 [5] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 [9] grid_2.14.1 gridExtra_0.9 MASS_7.3-17 memoise_0.1 [13] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [17] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.6.3 RSQLite_0.11.1 [21] rtracklayer_1.14.4 scales_0.2.0 stringr_0.6 tools_2.14.1 [25] XML_3.9-4 zlibbioc_1.0.1

sessionInfo() R version 2.15.0 beta (2012-03-20 r58793) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 [2] GenomicFeatures_1.7.33 [3] AnnotationDbi_1.17.27 [4] Biobase_2.15.4 [5] GenomicRanges_1.7.36 [6] IRanges_1.13.31 [7] BiocGenerics_0.1.14 [8] ggbio_1.1.7 [9] ggplot2_0.9.0 [10] devtools_0.6 [11] BiocInstaller_1.3.7

loaded via a namespace (and not attached): [1] biomaRt_2.11.2 Biostrings_2.23.6 biovizBase_1.1.12 bitops_1.0-4.1 [5] BSgenome_1.23.4 cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5 [9] dichromat_1.2-4 digest_0.5.2 grid_2.15.0 gridExtra_0.9 [13] Hmisc_3.9-2 lattice_0.20-6 MASS_7.3-17 memoise_0.1 [17] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [21] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.7.40 RSQLite_0.11.1 [25] rtracklayer_1.15.7 scales_0.2.0 stats4_2.15.0 stringr_0.6 [29] tcltk_2.15.0 tools_2.15.0 XML_3.9-4 zlibbioc_1.1.1

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name

nbartonicek commented 12 years ago

Hi Tengfei,

Thank you very much for your reply! Managed to make it work, and it should al be fine now. I've also spread the news about your package to the whole PhD community here, since I find it quite amazing.

Good work!

Cheers,

Nenad

On 21 Mar 2012, at 17:02, Tengfei Yin wrote:

Hi Nenad,

Thanks for reporting this issue, sorry that in the new ggbio, "qplot" will be dropped, and new "autoplot" will be the new generic function, that is based on recent ggplot2 udpate(0.9 have a autoplot generic function).

please get back later after this Friday(which is deadline for release for bioc 2.10), most part of the old vignette(in the intro.pdf) would be gone, please check the website later

http://tengfei.github.com/ggbio

I currently only updated the geom part in tutorial, by friday, most part in tutorial will be updated. So in the future, I will put documentation tutorial on-line.

I will get back to this issue on Friday and give you a new example for that.

Thanks

Tengfei

On Wed, Mar 21, 2012 at 7:21 AM, nbartonicek < reply@reply.github.com

wrote:

Hi,

I was having problems with the basic functionality of plotting exons. The error (copied code from the intro.pdf) I was getting was:

library(TxDb.Hsapiens.UCSC.hg19.knownGene) data(genesymbol) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene exons.tx <- exonsBy(txdb, by = "tx") exons.rbm17 <- subsetByOverlaps(exons.tx, genesymbol["RBM17"]) nms <- names(exons.rbm17) freqs <- c(100, 200, 300) names(freqs) <- nms p.splice1 <- qplot(exons.rbm17) Error in continuous_scale("size", "size_c", rescale_pal(range), ...) : unused argument(s) (to = c(5, 17))

The sessionInfo() is below. It was 2.14.1. R as in the sessionInfo of the vignette.

Then I installed the new beta R 2.15 and the developer's ggbio. I get two messages:

  1. dataset genesymbol is missing
  2. Examples 3.3.2. and 3.4. from intro.pdf do not work - I can't perform overlap with GRanges or IRanges:

ir <- ranges(gr[seqnames(gr) == "chr1"])[1:3] p1 <- qplot(ir) + opts(title = "full") p1 Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class 'structure("IRanges", package = "IRanges")' into a data.frame

Hope this helps.

Cheers,

Nenad

sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 [2] GenomicFeatures_1.6.8 [3] AnnotationDbi_1.16.19 [4] Biobase_2.14.0 [5] BiocInstaller_1.2.1 [6] GenomicRanges_1.6.7 [7] IRanges_1.12.6 [8] ggbio_1.0.4 [9] ggplot2_0.9.0 [10] biovizBase_1.0.4

loaded via a namespace (and not attached): [1] biomaRt_2.10.0 Biostrings_2.22.0 bitops_1.0-4.1 BSgenome_1.22.0 [5] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 [9] grid_2.14.1 gridExtra_0.9 MASS_7.3-17 memoise_0.1 [13] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [17] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.6.3 RSQLite_0.11.1 [21] rtracklayer_1.14.4 scales_0.2.0 stringr_0.6 tools_2.14.1 [25] XML_3.9-4 zlibbioc_1.0.1

sessionInfo() R version 2.15.0 beta (2012-03-20 r58793) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 [2] GenomicFeatures_1.7.33 [3] AnnotationDbi_1.17.27 [4] Biobase_2.15.4 [5] GenomicRanges_1.7.36 [6] IRanges_1.13.31 [7] BiocGenerics_0.1.14 [8] ggbio_1.1.7 [9] ggplot2_0.9.0 [10] devtools_0.6 [11] BiocInstaller_1.3.7

loaded via a namespace (and not attached): [1] biomaRt_2.11.2 Biostrings_2.23.6 biovizBase_1.1.12 bitops_1.0-4.1 [5] BSgenome_1.23.4 cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5 [9] dichromat_1.2-4 digest_0.5.2 grid_2.15.0 gridExtra_0.9 [13] Hmisc_3.9-2 lattice_0.20-6 MASS_7.3-17 memoise_0.1 [17] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [21] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.7.40 RSQLite_0.11.1 [25] rtracklayer_1.15.7 scales_0.2.0 stats4_2.15.0 stringr_0.6 [29] tcltk_2.15.0 tools_2.15.0 XML_3.9-4 zlibbioc_1.1.1

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10#issuecomment-4621897

Nenad Bartonicek PhD student, Enright group European Bioinformatics Institute Hinxton Cambridge CB10 1SD United Kingdom tel: +44-783-346-4280

nbartonicek commented 12 years ago

p.s. Just a small question... It would be very useful to represent the coverage on both the positive and the negative strand. Would it be possible to add this to the future versions?

On 21 Mar 2012, at 17:02, Tengfei Yin wrote:

Hi Nenad,

Thanks for reporting this issue, sorry that in the new ggbio, "qplot" will be dropped, and new "autoplot" will be the new generic function, that is based on recent ggplot2 udpate(0.9 have a autoplot generic function).

please get back later after this Friday(which is deadline for release for bioc 2.10), most part of the old vignette(in the intro.pdf) would be gone, please check the website later

http://tengfei.github.com/ggbio

I currently only updated the geom part in tutorial, by friday, most part in tutorial will be updated. So in the future, I will put documentation tutorial on-line.

I will get back to this issue on Friday and give you a new example for that.

Thanks

Tengfei

On Wed, Mar 21, 2012 at 7:21 AM, nbartonicek < reply@reply.github.com

wrote:

Hi,

I was having problems with the basic functionality of plotting exons. The error (copied code from the intro.pdf) I was getting was:

library(TxDb.Hsapiens.UCSC.hg19.knownGene) data(genesymbol) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene exons.tx <- exonsBy(txdb, by = "tx") exons.rbm17 <- subsetByOverlaps(exons.tx, genesymbol["RBM17"]) nms <- names(exons.rbm17) freqs <- c(100, 200, 300) names(freqs) <- nms p.splice1 <- qplot(exons.rbm17) Error in continuous_scale("size", "size_c", rescale_pal(range), ...) : unused argument(s) (to = c(5, 17))

The sessionInfo() is below. It was 2.14.1. R as in the sessionInfo of the vignette.

Then I installed the new beta R 2.15 and the developer's ggbio. I get two messages:

  1. dataset genesymbol is missing
  2. Examples 3.3.2. and 3.4. from intro.pdf do not work - I can't perform overlap with GRanges or IRanges:

ir <- ranges(gr[seqnames(gr) == "chr1"])[1:3] p1 <- qplot(ir) + opts(title = "full") p1 Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class 'structure("IRanges", package = "IRanges")' into a data.frame

Hope this helps.

Cheers,

Nenad

sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 [2] GenomicFeatures_1.6.8 [3] AnnotationDbi_1.16.19 [4] Biobase_2.14.0 [5] BiocInstaller_1.2.1 [6] GenomicRanges_1.6.7 [7] IRanges_1.12.6 [8] ggbio_1.0.4 [9] ggplot2_0.9.0 [10] biovizBase_1.0.4

loaded via a namespace (and not attached): [1] biomaRt_2.10.0 Biostrings_2.22.0 bitops_1.0-4.1 BSgenome_1.22.0 [5] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 [9] grid_2.14.1 gridExtra_0.9 MASS_7.3-17 memoise_0.1 [13] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [17] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.6.3 RSQLite_0.11.1 [21] rtracklayer_1.14.4 scales_0.2.0 stringr_0.6 tools_2.14.1 [25] XML_3.9-4 zlibbioc_1.0.1

sessionInfo() R version 2.15.0 beta (2012-03-20 r58793) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 [2] GenomicFeatures_1.7.33 [3] AnnotationDbi_1.17.27 [4] Biobase_2.15.4 [5] GenomicRanges_1.7.36 [6] IRanges_1.13.31 [7] BiocGenerics_0.1.14 [8] ggbio_1.1.7 [9] ggplot2_0.9.0 [10] devtools_0.6 [11] BiocInstaller_1.3.7

loaded via a namespace (and not attached): [1] biomaRt_2.11.2 Biostrings_2.23.6 biovizBase_1.1.12 bitops_1.0-4.1 [5] BSgenome_1.23.4 cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5 [9] dichromat_1.2-4 digest_0.5.2 grid_2.15.0 gridExtra_0.9 [13] Hmisc_3.9-2 lattice_0.20-6 MASS_7.3-17 memoise_0.1 [17] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [21] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.7.40 RSQLite_0.11.1 [25] rtracklayer_1.15.7 scales_0.2.0 stats4_2.15.0 stringr_0.6 [29] tcltk_2.15.0 tools_2.15.0 XML_3.9-4 zlibbioc_1.1.1

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10#issuecomment-4621897

tengfei commented 12 years ago

Hi Nenad,

Mmm..I will reopen this issue and add something to it before this Friday, the easiest way I can think about now is support facets by strand like autoplot(gr, facets = strand ~ seqnames, stat = "coverage", geom = "line")

I thought it should work, actually it won't now, because I set strict checking on data and only looks for faceting variables in element Metadata columns, clearly this should be fixed...

I will let you know when I check in a fix for that.

Thanks

Tengfei

On Wed, Mar 21, 2012 at 12:14 PM, nbartonicek < reply@reply.github.com

wrote:

p.s. Just a small question... It would be very useful to represent the coverage on both the positive and the negative strand. Would it be possible to add this to the future versions?

On 21 Mar 2012, at 17:02, Tengfei Yin wrote:

Hi Nenad,

Thanks for reporting this issue, sorry that in the new ggbio, "qplot" will be dropped, and new "autoplot" will be the new generic function, that is based on recent ggplot2 udpate(0.9 have a autoplot generic function).

please get back later after this Friday(which is deadline for release for bioc 2.10), most part of the old vignette(in the intro.pdf) would be gone, please check the website later

http://tengfei.github.com/ggbio

I currently only updated the geom part in tutorial, by friday, most part in tutorial will be updated. So in the future, I will put documentation tutorial on-line.

I will get back to this issue on Friday and give you a new example for that.

Thanks

Tengfei

On Wed, Mar 21, 2012 at 7:21 AM, nbartonicek < reply@reply.github.com

wrote:

Hi,

I was having problems with the basic functionality of plotting exons. The error (copied code from the intro.pdf) I was getting was:

library(TxDb.Hsapiens.UCSC.hg19.knownGene) data(genesymbol) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene exons.tx <- exonsBy(txdb, by = "tx") exons.rbm17 <- subsetByOverlaps(exons.tx, genesymbol["RBM17"]) nms <- names(exons.rbm17) freqs <- c(100, 200, 300) names(freqs) <- nms p.splice1 <- qplot(exons.rbm17) Error in continuous_scale("size", "size_c", rescale_pal(range), ...) : unused argument(s) (to = c(5, 17))

The sessionInfo() is below. It was 2.14.1. R as in the sessionInfo of the vignette.

Then I installed the new beta R 2.15 and the developer's ggbio. I get two messages:

  1. dataset genesymbol is missing
  2. Examples 3.3.2. and 3.4. from intro.pdf do not work - I can't perform overlap with GRanges or IRanges:

ir <- ranges(gr[seqnames(gr) == "chr1"])[1:3] p1 <- qplot(ir) + opts(title = "full") p1 Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class 'structure("IRanges", package = "IRanges")' into a data.frame

Hope this helps.

Cheers,

Nenad

sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 [2] GenomicFeatures_1.6.8 [3] AnnotationDbi_1.16.19 [4] Biobase_2.14.0 [5] BiocInstaller_1.2.1 [6] GenomicRanges_1.6.7 [7] IRanges_1.12.6 [8] ggbio_1.0.4 [9] ggplot2_0.9.0 [10] biovizBase_1.0.4

loaded via a namespace (and not attached): [1] biomaRt_2.10.0 Biostrings_2.22.0 bitops_1.0-4.1 BSgenome_1.22.0 [5] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 [9] grid_2.14.1 gridExtra_0.9 MASS_7.3-17 memoise_0.1 [13] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [17] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.6.3 RSQLite_0.11.1 [21] rtracklayer_1.14.4 scales_0.2.0 stringr_0.6 tools_2.14.1 [25] XML_3.9-4 zlibbioc_1.0.1

sessionInfo() R version 2.15.0 beta (2012-03-20 r58793) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 [2] GenomicFeatures_1.7.33 [3] AnnotationDbi_1.17.27 [4] Biobase_2.15.4 [5] GenomicRanges_1.7.36 [6] IRanges_1.13.31 [7] BiocGenerics_0.1.14 [8] ggbio_1.1.7 [9] ggplot2_0.9.0 [10] devtools_0.6 [11] BiocInstaller_1.3.7

loaded via a namespace (and not attached): [1] biomaRt_2.11.2 Biostrings_2.23.6 biovizBase_1.1.12 bitops_1.0-4.1 [5] BSgenome_1.23.4 cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5 [9] dichromat_1.2-4 digest_0.5.2 grid_2.15.0 gridExtra_0.9 [13] Hmisc_3.9-2 lattice_0.20-6 MASS_7.3-17 memoise_0.1 [17] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [21] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.7.40 RSQLite_0.11.1 [25] rtracklayer_1.15.7 scales_0.2.0 stats4_2.15.0 stringr_0.6 [29] tcltk_2.15.0 tools_2.15.0 XML_3.9-4 zlibbioc_1.1.1

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10#issuecomment-4621897

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10#issuecomment-4622150

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name

nbartonicek commented 12 years ago

Hi Tengfei,

Brilliant! Thanks a bunch... Just to let you know, I've already sent a recommendation to my friends outside of the country... I'll also advertise your package in the Next Gen Visualization seminars we have here.

Best,

Nenad

On 21 Mar 2012, at 17:33, Tengfei Yin wrote:

Hi Nenad,

Mmm..I will reopen this issue and add something to it before this Friday, the easiest way I can think about now is support facets by strand like autoplot(gr, facets = strand ~ seqnames, stat = "coverage", geom = "line")

I thought it should work, actually it won't now, because I set strict checking on data and only looks for faceting variables in element Metadata columns, clearly this should be fixed...

I will let you know when I check in a fix for that.

Thanks

Tengfei

On Wed, Mar 21, 2012 at 12:14 PM, nbartonicek < reply@reply.github.com

wrote:

p.s. Just a small question... It would be very useful to represent the coverage on both the positive and the negative strand. Would it be possible to add this to the future versions?

On 21 Mar 2012, at 17:02, Tengfei Yin wrote:

Hi Nenad,

Thanks for reporting this issue, sorry that in the new ggbio, "qplot" will be dropped, and new "autoplot" will be the new generic function, that is based on recent ggplot2 udpate(0.9 have a autoplot generic function).

please get back later after this Friday(which is deadline for release for bioc 2.10), most part of the old vignette(in the intro.pdf) would be gone, please check the website later

http://tengfei.github.com/ggbio

I currently only updated the geom part in tutorial, by friday, most part in tutorial will be updated. So in the future, I will put documentation tutorial on-line.

I will get back to this issue on Friday and give you a new example for that.

Thanks

Tengfei

On Wed, Mar 21, 2012 at 7:21 AM, nbartonicek < reply@reply.github.com

wrote:

Hi,

I was having problems with the basic functionality of plotting exons. The error (copied code from the intro.pdf) I was getting was:

library(TxDb.Hsapiens.UCSC.hg19.knownGene) data(genesymbol) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene exons.tx <- exonsBy(txdb, by = "tx") exons.rbm17 <- subsetByOverlaps(exons.tx, genesymbol["RBM17"]) nms <- names(exons.rbm17) freqs <- c(100, 200, 300) names(freqs) <- nms p.splice1 <- qplot(exons.rbm17) Error in continuous_scale("size", "size_c", rescale_pal(range), ...) : unused argument(s) (to = c(5, 17))

The sessionInfo() is below. It was 2.14.1. R as in the sessionInfo of the vignette.

Then I installed the new beta R 2.15 and the developer's ggbio. I get two messages:

  1. dataset genesymbol is missing
  2. Examples 3.3.2. and 3.4. from intro.pdf do not work - I can't perform overlap with GRanges or IRanges:

ir <- ranges(gr[seqnames(gr) == "chr1"])[1:3] p1 <- qplot(ir) + opts(title = "full") p1 Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class 'structure("IRanges", package = "IRanges")' into a data.frame

Hope this helps.

Cheers,

Nenad

sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 [2] GenomicFeatures_1.6.8 [3] AnnotationDbi_1.16.19 [4] Biobase_2.14.0 [5] BiocInstaller_1.2.1 [6] GenomicRanges_1.6.7 [7] IRanges_1.12.6 [8] ggbio_1.0.4 [9] ggplot2_0.9.0 [10] biovizBase_1.0.4

loaded via a namespace (and not attached): [1] biomaRt_2.10.0 Biostrings_2.22.0 bitops_1.0-4.1 BSgenome_1.22.0 [5] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 [9] grid_2.14.1 gridExtra_0.9 MASS_7.3-17 memoise_0.1 [13] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [17] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.6.3 RSQLite_0.11.1 [21] rtracklayer_1.14.4 scales_0.2.0 stringr_0.6 tools_2.14.1 [25] XML_3.9-4 zlibbioc_1.0.1

sessionInfo() R version 2.15.0 beta (2012-03-20 r58793) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 [2] GenomicFeatures_1.7.33 [3] AnnotationDbi_1.17.27 [4] Biobase_2.15.4 [5] GenomicRanges_1.7.36 [6] IRanges_1.13.31 [7] BiocGenerics_0.1.14 [8] ggbio_1.1.7 [9] ggplot2_0.9.0 [10] devtools_0.6 [11] BiocInstaller_1.3.7

loaded via a namespace (and not attached): [1] biomaRt_2.11.2 Biostrings_2.23.6 biovizBase_1.1.12 bitops_1.0-4.1 [5] BSgenome_1.23.4 cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5 [9] dichromat_1.2-4 digest_0.5.2 grid_2.15.0 gridExtra_0.9 [13] Hmisc_3.9-2 lattice_0.20-6 MASS_7.3-17 memoise_0.1 [17] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [21] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.7.40 RSQLite_0.11.1 [25] rtracklayer_1.15.7 scales_0.2.0 stats4_2.15.0 stringr_0.6 [29] tcltk_2.15.0 tools_2.15.0 XML_3.9-4 zlibbioc_1.1.1

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10#issuecomment-4621897

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10#issuecomment-4622150

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name

Reply to this email directly or view it on GitHub: https://github.com/tengfei/ggbio/issues/10#issuecomment-4622588

Nenad Bartonicek PhD student, Enright group European Bioinformatics Institute Hinxton Cambridge CB10 1SD United Kingdom tel: +44-783-346-4280