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gladkia / igvR

An R Bioconductor package providing interactive connections to igv.js (the Integrative Genomics Viewer) in a web browser
MIT License
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svg file, right thumbinal but wrong svg #13

Closed alessandriLuca closed 2 years ago

alessandriLuca commented 3 years ago

Hi, i would like to compliment on this work. Is great! definetly better then the normal igv browser. Im planning to use it a lot. I have some trouble on svg saving from both the browser and from the code it give me the same results. So apparently when i load a bedgraph with negative value they are displayed on the browser, then i save everything on svg and here is the problem, positive value of bedgraph are fine, negative just disappear. Another funny thing is that in the thumbinal of the svg i can definetly see the negative value. Here is an example of svg file Also here are the version of the libraries installed in my R environment. As browser im using firefox 88.0 (64-bit) on Kubuntu 20.04.2 LTS. (I also tried Chromium but i have the same issue)

R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] rtracklayer_1.46.0 AnnotationHub_2.18.0
[3] BiocFileCache_1.10.2 dbplyr_2.1.1
[5] VariantAnnotation_1.32.0 igvR_1.11.2
[7] BrowserViz_2.12.0 httpuv_1.6.0
[9] jsonlite_1.7.2 GenomicAlignments_1.22.1
[11] Rsamtools_2.2.3 Biostrings_2.54.0
[13] XVector_0.26.0 SummarizedExperiment_1.16.1 [15] DelayedArray_0.12.3 BiocParallel_1.20.1
[17] matrixStats_0.58.0 Biobase_2.46.0
[19] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[21] IRanges_2.20.2 S4Vectors_0.24.4
[23] BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] httr_1.4.2 bit64_4.0.5
[3] shiny_1.6.0 assertthat_0.2.1
[5] interactiveDisplayBase_1.24.0 askpass_1.1
[7] BiocManager_1.30.12 blob_1.2.1
[9] BSgenome_1.54.0 GenomeInfoDbData_1.2.2
[11] yaml_2.2.1 progress_1.2.2
[13] BiocVersion_3.10.1 pillar_1.6.0
[15] RSQLite_2.2.7 lattice_0.20-44
[17] glue_1.4.2 digest_0.6.27
[19] RColorBrewer_1.1-2 promises_1.2.0.1
[21] htmltools_0.5.1.1 Matrix_1.3-3
[23] XML_3.99-0.3 pkgconfig_2.0.3
[25] biomaRt_2.42.1 zlibbioc_1.32.0
[27] xtable_1.8-4 purrr_0.3.4
[29] later_1.2.0 tibble_3.1.1
[31] openssl_1.4.4 generics_0.1.0
[33] ellipsis_0.3.2 cachem_1.0.4
[35] GenomicFeatures_1.38.2 mime_0.10
[37] splitstackshape_1.4.8 magrittr_2.0.1
[39] crayon_1.4.1 memoise_2.0.0
[41] fansi_0.4.2 tools_3.6.3
[43] data.table_1.14.0 prettyunits_1.1.1
[45] hms_1.0.0 lifecycle_1.0.0
[47] stringr_1.4.0 AnnotationDbi_1.48.0
[49] compiler_3.6.3 rlang_0.4.11
[51] MotifDb_1.28.0 grid_3.6.3
[53] RCurl_1.98-1.3 rappdirs_0.3.3
[55] bitops_1.0-7 DBI_1.1.1
[57] curl_4.3.1 R6_2.5.0
[59] seqLogo_1.52.0 dplyr_1.0.5
[61] fastmap_1.1.0 bit_4.0.4
[63] utf8_1.2.1 stringi_1.5.3
[65] Rcpp_1.0.6 vctrs_0.3.8
[67] tidyselect_1.1.1

Thank you

Best

paul-shannon commented 3 years ago

Traveling now, will look on Saturday. Thanks for the report!

Sent from my iPhone

On May 5, 2021, at 7:12 AM, alessandriLuca @.***> wrote:

 Hi, i would like to compliment on this work. Is great! definetly better then the normal igv browser. Im planning to use it a lot. I have some trouble on svg saving from both the browser and from the code it give me the same results. So apparently when i load a bedgraph with negative value they are displayed on the browser, then i save everything on svg and here is the problem, positive value of bedgraph are fine, negative just disappear. Another funny thing is that in the thumbinal of the svg i can definetly see the negative value. Here is an example of svg file Also here are the version of the libraries installed in my R environment. As browser im using firefox 88.0 (64-bit) on Kubuntu 20.04.2 LTS.

R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] rtracklayer_1.46.0 AnnotationHub_2.18.0 [3] BiocFileCache_1.10.2 dbplyr_2.1.1 [5] VariantAnnotation_1.32.0 igvR_1.11.2 [7] BrowserViz_2.12.0 httpuv_1.6.0 [9] jsonlite_1.7.2 GenomicAlignments_1.22.1 [11] Rsamtools_2.2.3 Biostrings_2.54.0 [13] XVector_0.26.0 SummarizedExperiment_1.16.1 [15] DelayedArray_0.12.3 BiocParallel_1.20.1 [17] matrixStats_0.58.0 Biobase_2.46.0 [19] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 [21] IRanges_2.20.2 S4Vectors_0.24.4 [23] BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] httr_1.4.2 bit64_4.0.5 [3] shiny_1.6.0 assertthat_0.2.1 [5] interactiveDisplayBase_1.24.0 askpass_1.1 [7] BiocManager_1.30.12 blob_1.2.1 [9] BSgenome_1.54.0 GenomeInfoDbData_1.2.2 [11] yaml_2.2.1 progress_1.2.2 [13] BiocVersion_3.10.1 pillar_1.6.0 [15] RSQLite_2.2.7 lattice_0.20-44 [17] glue_1.4.2 digest_0.6.27 [19] RColorBrewer_1.1-2 promises_1.2.0.1 [21] htmltools_0.5.1.1 Matrix_1.3-3 [23] XML_3.99-0.3 pkgconfig_2.0.3 [25] biomaRt_2.42.1 zlibbioc_1.32.0 [27] xtable_1.8-4 purrr_0.3.4 [29] later_1.2.0 tibble_3.1.1 [31] openssl_1.4.4 generics_0.1.0 [33] ellipsis_0.3.2 cachem_1.0.4 [35] GenomicFeatures_1.38.2 mime_0.10 [37] splitstackshape_1.4.8 magrittr_2.0.1 [39] crayon_1.4.1 memoise_2.0.0 [41] fansi_0.4.2 tools_3.6.3 [43] data.table_1.14.0 prettyunits_1.1.1 [45] hms_1.0.0 lifecycle_1.0.0 [47] stringr_1.4.0 AnnotationDbi_1.48.0 [49] compiler_3.6.3 rlang_0.4.11 [51] MotifDb_1.28.0 grid_3.6.3 [53] RCurl_1.98-1.3 rappdirs_0.3.3 [55] bitops_1.0-7 DBI_1.1.1 [57] curl_4.3.1 R6_2.5.0 [59] seqLogo_1.52.0 dplyr_1.0.5 [61] fastmap_1.1.0 bit_4.0.4 [63] utf8_1.2.1 stringi_1.5.3 [65] Rcpp_1.0.6 vctrs_0.3.8 [67] tidyselect_1.1.1

Thank you

Best

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paul-shannon commented 3 years ago

I had hoped to take a look at this during a brief stay in Boulder, but failed to do so.

I will be home on May 16th, and promise to look at this then.

On May 5, 2021, at 12:49 PM, Paul Shannon @.***> wrote:

Traveling now, will look on Saturday. Thanks for the report!

Sent from my iPhone

On May 5, 2021, at 7:12 AM, alessandriLuca @.***> wrote:

 Hi, i would like to compliment on this work. Is great! definetly better then the normal igv browser. Im planning to use it a lot. I have some trouble on svg saving from both the browser and from the code it give me the same results. So apparently when i load a bedgraph with negative value they are displayed on the browser, then i save everything on svg and here is the problem, positive value of bedgraph are fine, negative just disappear. Another funny thing is that in the thumbinal of the svg i can definetly see the negative value. Here is an example of svg file Also here are the version of the libraries installed in my R environment. As browser im using firefox 88.0 (64-bit) on Kubuntu 20.04.2 LTS.

R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] rtracklayer_1.46.0 AnnotationHub_2.18.0 [3] BiocFileCache_1.10.2 dbplyr_2.1.1 [5] VariantAnnotation_1.32.0 igvR_1.11.2 [7] BrowserViz_2.12.0 httpuv_1.6.0 [9] jsonlite_1.7.2 GenomicAlignments_1.22.1 [11] Rsamtools_2.2.3 Biostrings_2.54.0 [13] XVector_0.26.0 SummarizedExperiment_1.16.1 [15] DelayedArray_0.12.3 BiocParallel_1.20.1 [17] matrixStats_0.58.0 Biobase_2.46.0 [19] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 [21] IRanges_2.20.2 S4Vectors_0.24.4 [23] BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] httr_1.4.2 bit64_4.0.5 [3] shiny_1.6.0 assertthat_0.2.1 [5] interactiveDisplayBase_1.24.0 askpass_1.1 [7] BiocManager_1.30.12 blob_1.2.1 [9] BSgenome_1.54.0 GenomeInfoDbData_1.2.2 [11] yaml_2.2.1 progress_1.2.2 [13] BiocVersion_3.10.1 pillar_1.6.0 [15] RSQLite_2.2.7 lattice_0.20-44 [17] glue_1.4.2 digest_0.6.27 [19] RColorBrewer_1.1-2 promises_1.2.0.1 [21] htmltools_0.5.1.1 Matrix_1.3-3 [23] XML_3.99-0.3 pkgconfig_2.0.3 [25] biomaRt_2.42.1 zlibbioc_1.32.0 [27] xtable_1.8-4 purrr_0.3.4 [29] later_1.2.0 tibble_3.1.1 [31] openssl_1.4.4 generics_0.1.0 [33] ellipsis_0.3.2 cachem_1.0.4 [35] GenomicFeatures_1.38.2 mime_0.10 [37] splitstackshape_1.4.8 magrittr_2.0.1 [39] crayon_1.4.1 memoise_2.0.0 [41] fansi_0.4.2 tools_3.6.3 [43] data.table_1.14.0 prettyunits_1.1.1 [45] hms_1.0.0 lifecycle_1.0.0 [47] stringr_1.4.0 AnnotationDbi_1.48.0 [49] compiler_3.6.3 rlang_0.4.11 [51] MotifDb_1.28.0 grid_3.6.3 [53] RCurl_1.98-1.3 rappdirs_0.3.3 [55] bitops_1.0-7 DBI_1.1.1 [57] curl_4.3.1 R6_2.5.0 [59] seqLogo_1.52.0 dplyr_1.0.5 [61] fastmap_1.1.0 bit_4.0.4 [63] utf8_1.2.1 stringi_1.5.3 [65] Rcpp_1.0.6 vctrs_0.3.8 [67] tidyselect_1.1.1

Thank you

Best

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alessandriLuca commented 3 years ago

Hi, no worries, right now I solved with automatic screenshot xD so i can use it anyway! Take your time and thanks again!

alessandriLuca commented 3 years ago

I Also have another question, is there any way in which i can disable track labels? From the browser i can unselect the option but i wasnt able to find anything related to that in the igvR code. Thank you again

Best

Luca

paul-shannon commented 3 years ago

@alessandriLuca I upgraded (this is long overdue) to igv.js 2.8.2, and igvR::getSvg() now works better. But still not quite right.

See new issue at github igv.jssvg of +/- bedgraph lacks the zero line (chrom, safari, firefox) #1332.

I will update again once Jim Robinson solves this problem - or shows me that it is my error :)

Many thanks for the bug report!

alessandriLuca commented 3 years ago

@paul-shannon many thanks for your work! Can i leave this open as a remind for when it will be totally fixed?

Thank you again and, again congratulation for the great job ;) is super usefull!!

Best

Luca

paul-shannon commented 3 years ago

Yes, please leave it open.

Programmatic show/hide track labels goes in today.

Great to have your reports and requests!

On May 24, 2021, at 7:26 AM, alessandriLuca @.***> wrote:

@paul-shannon many thanks for your work! Can i leave this open as a remind for when it will be totally fixed?

Thank you again and, again congratulation for the great job ;) is super usefull!!

Best

Luca

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paul-shannon commented 2 years ago

Just verified that showTrackLabels(igv, TRUE|FALSE) works, so closing this belatedly.