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showteeth
Error when running ggcoverage() examples
Hello, I have installed the ggcoverage and currently testing this package running ggcoverage() examples. But the problem arose when I wanted to draw an ideogram, here's the error message: Loading ideogram... Error in normArgTrack(track, trackids) : Unknown track: cytoBand cytoBand informatin is not available, only get ranges. Loading ranges... Done Error in .local(data, ...) : Need cytoband information, please check the getIdeogram function
Thank you for developing ggcoverage and providing me with a great tool for visualizing genes and variation information. I also appreciate your help in solving this problem.
Best, Yanze
Sure, and thanks for your attention. The code was constant with the manual of ggcoverage (RNA-seq data) showed in github. And here is the details: #test library("rtracklayer") library("ggcoverage") library("ggpattern")
load metadata
meta.file <- system.file("extdata", "RNA-seq", "meta_info.csv", package = "ggcoverage") sample.meta = read.csv(meta.file)
track folder
track.folder = system.file("extdata", "RNA-seq", package = "ggcoverage")
load bigwig file
track.df = LoadTrackFile(track.folder = track.folder, format = "bw", region = "chr14:21,677,306-21,737,601", extend = 2000, meta.info = sample.meta)
create mark region
mark.region=data.frame(start=c(21678900,21732001,21737590), end=c(21679900,21732400,21737650), label=c("M1", "M2", "M3")) #Load GTF gtf.file = system.file("extdata", "used_hg19.gtf", package = "ggcoverage") gtf.gr = rtracklayer::import.gff(con = gtf.file, format = 'gtf') #Basic coverage basic.coverage = ggcoverage(data = track.df, plot.type = "facet", mark.region = mark.region, range.position = "out") basic.coverage #add ideogram basic.coverage + geom_gene(gtf.gr=gtf.gr) + geom_ideogram(genome = "hg19",plot.space = 0)
Thank you
I just put the example code here again in clean form. This works for me out of the box using the latest version of ggcoverage with some fixes:
library("rtracklayer")
library("ggcoverage")
library("ggpattern")
# load metadata
meta.file <- system.file("extdata", "RNA-seq", "meta_info.csv", package = "ggcoverage")
sample.meta = read.csv(meta.file)
# track folder
track.folder = system.file("extdata", "RNA-seq", package = "ggcoverage")
# load bigwig file
track.df = LoadTrackFile(track.folder = track.folder, format = "bw",
region = "chr14:21,677,306-21,737,601", extend = 2000,
meta.info = sample.meta)
# create mark region
mark.region=data.frame(start=c(21678900,21732001,21737590),
end=c(21679900,21732400,21737650),
label=c("M1", "M2", "M3"))
# load GTF
gtf.file = system.file("extdata", "used_hg19.gtf", package = "ggcoverage")
gtf.gr = rtracklayer::import.gff(con = gtf.file, format = 'gtf')
# basic coverage
basic.coverage = ggcoverage(data = track.df, plot.type = "facet",
mark.region = mark.region, range.position = "out")
basic.coverage
#add ideogram
basic.coverage +
geom_gene(gtf.gr=gtf.gr) +
geom_ideogram(genome = "hg19",plot.space = 0)
Try to install ggcoverage from my fork using:
remotes::install_github("https://github.com/m-jahn/ggcoverage", ref = "colors")
Try to install the dependencies of the package if it still fails.
Result:
Sorry for taking so long to reply to you. I have run the code you provided above and still encounter the same problem as before. Loading ideogram... Error in normArgTrack(track, trackids) : Unknown track: cytoBand cytoBand informatin is not available, only get ranges. Loading ranges... Done Error in .local(data, ...) : Need cytoband information, please check the getIdeogram function
since it works on my end with the latest package installs, the problem must be your local system: Have you re-installed ggcoverage from my fork?
remotes::install_github("https://github.com/m-jahn/ggcoverage", ref = "colors")
Have you installed all required dependencies of ggcoverage? Some of the examples require suggested packages that are not automatically installed as you are probably used to when installing a new package.
If you look into the DESCRIPTION file of the package you see all dependencies:
Imports:
dplyr,
GenomicRanges,
ggbio,
ggh4x,
ggplot2,
ggrepel,
grDevices,
IRanges,
magrittr,
patchwork,
RColorBrewer,
rlang,
Rsamtools,
rtracklayer,
scales,
stats,
utils,
methods,
GenomeInfoDb,
S4Vectors,
Biostrings,
BSgenome,
GenomicAlignments,
reshape2,
seqinr,
ggforce,
HiCBricks,
ggpattern,
BiocParallel,
openxlsx,
stringr,
ggpp
Suggests:
rmarkdown,
knitr,
BiocStyle,
htmltools,
BSgenome.Hsapiens.UCSC.hg19,
graphics,
HiCDataHumanIMR90
I know this is a long list; but try to install the Suggests and you should be good. Also, check that you are running a recent R version. I run 4.3.2.
@m-jahn
I cannot repeat the example on window10 too.
First time, remotes::install_github("showteeth/ggcoverage"), it gives the same error.
> basic.coverage +
+ geom_gc(bs.fa.seq=BSgenome.Hsapiens.UCSC.hg19) +
+ geom_gene(gtf.gr=gtf.gr) +
+ geom_ideogram(genome = "hg19")
Loading ideogram...
Error in normArgTrack(track, trackids) : Unknown track: cytoBand
cytoBand information is not available, only getting ranges.
Loading ranges...
Done
Error in .local(data, ...) :
Need cytoband information, please check the getIdeogram function
Second time,
> remotes::install_github("https://github.com/m-jahn/ggcoverage", ref = "colors")
Using GitHub PAT from the git credential store.
Downloading GitHub repo m-jahn/ggcoverage@colors
Error in utils::download.file(url, path, method = method, quiet = quiet, :
无法打开URL'https://api.github.com/repos/m-jahn/ggcoverage/tarball/colors'
Can you check it please ? Best, xiucz
Please Install the 'Suggested' packages, These are required to run geom_ideogram().
> library("BiocStyle")
> library("ggbio")
> library(HiCBricks)
> library(HiCDataHumanIMR90)
> library(BSgenome.Hsapiens.UCSC.hg19)
>
> basic.coverage +
+ geom_gc(bs.fa.seq=BSgenome.Hsapiens.UCSC.hg19) +
+ geom_gene(gtf.gr=gtf.gr) +
+ geom_ideogram(genome = "hg19")
Loading ideogram...
Error in normArgTrack(track, trackids) : Unknown track: cytoBand
cytoBand information is not available, only getting ranges.
Loading ranges...
Done
Error in .local(data, ...) :
Need cytoband information, please check the getIdeogram function
I review the source code, geom_ideogram() use the ggbio package to get the cytoband info. However, the package was installed.
https://rdrr.io/cran/ggcoverage/src/R/geom_ideogram.R#:~:text=genome.info%20%3C%2D%20suppressWarnings(getIdeogram(genome%20%3D%20genome%2C%20subchr%20%3D%20plot.chr%2C%20cytobands%20%3D%20TRUE))
Any further suggestions? thank you!
Best,
xiucz
OK, then I can only try to reproduce the issue. Can you post the output from SessionInfo()?
Restart my R4.3.3 on my window10 first , then
> suppressPackageStartupMessages({
library("ggcoverage")
library("BiocStyle")
library("ggbio")
library("BSgenome.Hsapiens.UCSC.hg19")
})
>
> SessionInfo()
Error in SessionInfo() : 没有"SessionInfo"这个函数
> sessionInfo()
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8
[2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.70.2
[3] rtracklayer_1.62.0 BiocIO_1.12.0
[5] Biostrings_2.70.3 XVector_0.42.0
[7] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8
[9] IRanges_2.36.0 S4Vectors_0.40.2
[11] ggbio_1.50.0 ggplot2_3.5.0
[13] BiocGenerics_0.48.1 BiocStyle_2.30.0
[15] ggcoverage_1.4.0
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.16.0
[3] magrittr_2.0.3 GenomicFeatures_1.54.4
[5] rmarkdown_2.26 zlibbioc_1.48.2
[7] vctrs_0.6.5 memoise_2.0.1
[9] Rsamtools_2.18.0 RCurl_1.98-1.14
[11] base64enc_0.1-3 htmltools_0.5.8.1
[13] S4Arrays_1.2.1 progress_1.2.3
[15] curl_5.2.1 SparseArray_1.2.4
[17] Formula_1.2-5 htmlwidgets_1.6.4
[19] plyr_1.8.9 cachem_1.0.8
[21] GenomicAlignments_1.38.2 lifecycle_1.0.4
[23] pkgconfig_2.0.3 Matrix_1.6-5
[25] R6_2.5.1 fastmap_1.1.1
[27] GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0
[29] digest_0.6.35 colorspace_2.1-0
[31] GGally_2.2.1 patchwork_1.2.0
[33] AnnotationDbi_1.64.1 OrganismDbi_1.44.0
[35] Hmisc_5.1-2 RSQLite_2.3.6
[37] filelock_1.0.3 fansi_1.0.6
[39] httr_1.4.7 abind_1.4-5
[41] compiler_4.3.3 bit64_4.0.5
[43] withr_3.0.0 htmlTable_2.4.2
[45] backports_1.4.1 BiocParallel_1.36.0
[47] DBI_1.2.2 ggstats_0.6.0
[49] biomaRt_2.58.2 rappdirs_0.3.3
[51] DelayedArray_0.28.0 rjson_0.2.21
[53] tools_4.3.3 foreign_0.8-86
[55] nnet_7.3-19 glue_1.7.0
[57] restfulr_0.0.15 grid_4.3.3
[59] checkmate_2.3.1 cluster_2.1.6
[61] reshape2_1.4.4 generics_0.1.3
[63] gtable_0.3.4 ggpattern_1.0.1
[65] tidyr_1.3.1 ensembldb_2.26.1
[67] data.table_1.15.4 hms_1.1.3
[69] xml2_1.3.6 utf8_1.2.4
[71] ggrepel_0.9.5 pillar_1.9.0
[73] stringr_1.5.1 dplyr_1.1.4
[75] BiocFileCache_2.10.2 lattice_0.22-5
[77] bit_4.0.5 biovizBase_1.50.0
[79] RBGL_1.78.0 tidyselect_1.2.1
[81] knitr_1.46 gridExtra_2.3
[83] ProtGenerics_1.34.0 SummarizedExperiment_1.32.0
[85] xfun_0.43 Biobase_2.62.0
[87] matrixStats_1.2.0 stringi_1.8.3
[89] lazyeval_0.2.2 yaml_2.3.8
[91] evaluate_0.23 codetools_0.2-19
[93] tibble_3.2.1 graph_1.80.0
[95] BiocManager_1.30.22 cli_3.6.2
[97] rpart_4.1.23 munsell_0.5.1
[99] dichromat_2.0-0.1 Rcpp_1.0.12
[101] dbplyr_2.5.0 png_0.1-8
[103] XML_3.99-0.16.1 parallel_4.3.3
[105] ggh4x_0.2.8 blob_1.2.4
[107] prettyunits_1.2.0 AnnotationFilter_1.26.0
[109] bitops_1.0-7 VariantAnnotation_1.48.1
[111] scales_1.3.0 purrr_1.0.2
[113] crayon_1.5.2 rlang_1.1.3
[115] KEGGREST_1.42.0
>
Best, xiucz
I can reproduce the error. There is a problem with the rtracklayer package getting cytoband (and other other types of info) from USCS databases. Cytoband information is fetched remotely, so we need both internet access and a working API on the server side. I try to look into this but it could be a server issue on their side.
check out the latest version from the linked repo above, it should fix the issue
remotes::install_github("https://github.com/m-jahn/ggcoverage/tree/dev")
^_^, I thought the problem was with ggbio packages, haha. Thank you for debugging it. Downloading databases from websites every time seems to be not a very reliable choice because once the website encounters issues or a poor network, the tool will be broken.
After the rebuild, it works. Best, xiucz