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A pure R implementation of locuszoom for plotting genetic data at genomic loci accompanied by gene annotations.

License: GNU General Public License v3.0

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twillis209 nickhir lukepilling oborisov huizhong1993

locuszoomr's Issues

Error in `check_breaks_labels()`: ! `breaks` and `labels` must have the same length

Hello,

I am using the latest version (locuszoomr_0.1.5 via devtools::install_github("myles-lewis/locuszoomr")) and encountered the following error when trying to run locus_ggplot:

Error in `check_breaks_labels()`:
! `breaks` and `labels` must have the same length

The interesting thing is, that locus_plot and locus_plotly work without any issue, so I dont think anything is "wrong" with the way I have prepared my data. I have

I have uploaded a small, randomized dataset (>50kb) with which one can reproduce the error:
https://we.tl/t-eBpXs3UVAh

tmp <- data.table::fread("path/to/file")
loc_test <- locus(
    data = as.data.frame(tmp),
    chrom = "Chr",
    pos = "bp",
    p = "pC",
    labs = "SNP",
    seqname = chr,
    flank = 0,
    xrange = c(start, stop),
    ens_db = "EnsDb.Hsapiens.v75",
    LD = "1_247603584_C_T"
)
locus_plot(loc_test) #works
locus_plotly(loc_test) #works
locus_ggplot(loc_test) #doesnt work

Thank you very much in advance!

error with link_recomb

I'm getting the following error message when using the link_recomb function:

APP.recomb <- link_recomb(APP.test)
Retrieving recombination data from UCSC
Error in normArgTable(value, x) : Table 'recomb1000GAvg' is unavailable

stacking gg_scatter plots on top of one another

Hello,

I am currently running a colocalization analysis between two traits. For this, I like to stack the plots on top of one another. This works perfectly with the example in your vignette:

library(locuszoomr)
data(SLE_gwas_sub)  ## limited subset of data from SLE GWAS
library(EnsDb.Hsapiens.v75)

loc <- locus(gene = 'UBE2L3', SLE_gwas_sub, flank = 1e5, ens_db = "EnsDb.Hsapiens.v75")
set_layers(2)
scatter_plot(loc)
scatter_plot(loc)
genetracks(loc)

However, in my case, I need to use gg_scatter instead of the scatter_plot option, because I need to do some slight modifications to my plot (I want to highlight certain points with circles and this is just much easier to do with a ggplot object). The problem that I am running into is, that when I have two ggplot objects, I cant properly align them above the gene tracks... Here is my code:

library(patchwork)
p1 <- gg_scatter(loc)
p2 <- gg_scatter(loc)
genes <- gg_genetracks(loc)
wrap_plots(p1,p2,genes, ncol=1)

Do you have any ideas how to accomplish this? I think it would be incredibly helpful because it would very much increase the flexiblity of the package.

genome build option for LD

Any chance you can include an option in the link_LD() function to choose the genome build as LDlinkR now supports multiple builds? Thanks!

link_recomb has curl errors

I did notice the other recent issue with the link_recomb function, but that seems to be separate to the issue I have encountered.

Essentially after running the following:

analysis_locus = locus(index_snp = currrsid, data = plot_frame, flank = 5e5,
                            chrom = "chr", pos = "pos", p = "p", ens_db = ensDb_v111)

analysis_locus_ld = link_LD(analysis_locus, token = "<MYTOKEN>")

analysis_locus_ld = link_recomb(analysis_locus_ld, genome = "hg38")

I got this in return:

Retrieving recombination data from UCSC
Warning messages:
1: In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) :
  Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x3b408e000): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
2: In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) :
  Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x3bf625180): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!

Making the LocusZoom plot with locus_plot still worked as expected and produced the same plots as before, with a "Recombination %" axis. However, there were no recombination rate blue lines within the plot.

Incidentally, this package is excellent! Really nice to use, thanks so much!

graph range in locuszoomr

Hello, I appreciate for this great tool.
I have several issues while I draw plots locuszoomr and arrange other plots with cowplot.

First, when I get recombination rate, it always return error.
Here is my code.

> loc <- locus(data = tb_1, seqname = 5, xrange = c(96207000, 96259000), flank = 1e5, ens_db = "EnsDb.Hsapiens.v75")
chromosome 5, position 96207000 to 96259000
186 SNPs/datapoints
> loc <- link_LD(loc, token = my_token)
Obtaining LD on 186 SNPs
LDlink server is working...
> tb_1$r2 <- loc$data$ld
> loc <- link_recomb(loc, genome = "hg19")
Retrieving recombination data from UCSC
Error in .local(object, ...) : tabular output format not available

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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

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

other attached packages:
[1] cowplot_1.1.1             EnsDb.Hsapiens.v75_2.99.0 ensembldb_2.10.2          AnnotationFilter_1.10.0   AnnotationHub_2.18.0     
[6] BiocFileCache_1.10.2      dbplyr_2.1.1              locuszoomr_0.2.1          GenomicFeatures_1.38.2    AnnotationDbi_1.48.0     
[11] Biobase_2.46.0            GenomicRanges_1.38.0      GenomeInfoDb_1.22.1       IRanges_2.20.2            S4Vectors_0.24.4         
[16] ggbio_1.34.0              ggplot2_3.5.0             BiocGenerics_0.32.0      

loaded via a namespace (and not attached):
[1] colorspace_2.0-2              ellipsis_0.3.2                biovizBase_1.34.1             htmlTable_2.4.1              
[5] XVector_0.26.0                base64enc_0.1-3               dichromat_2.0-0.1             rstudioapi_0.15.0            
[9] farver_2.1.0                  remotes_2.4.2.1               ggrepel_0.9.1                 bit64_4.0.5                  
[13] interactiveDisplayBase_1.24.0 fansi_0.5.0                   splines_3.6.3                 cachem_1.0.5                 
[17] knitr_1.45                    jsonlite_1.8.8                Formula_1.2-5                 Rsamtools_2.2.3              
[21] cluster_2.1.4                 png_0.1-7                     graph_1.64.0                  shiny_1.6.0                  
[25] BiocManager_1.30.22           compiler_3.6.3                httr_1.4.7                    backports_1.2.1              
[29] assertthat_0.2.1              Matrix_1.5-1                  fastmap_1.1.0                 lazyeval_0.2.2               
[33] cli_3.6.2                     later_1.2.0                   htmltools_0.5.7               prettyunits_1.1.1            
[37] tools_3.6.3                   gtable_0.3.0                  glue_1.7.0                    GenomeInfoDbData_1.2.2       
[41] reshape2_1.4.4                dplyr_1.1.4                   rappdirs_0.3.3                Rcpp_1.0.7                   
[45] vctrs_0.6.5                   Biostrings_2.54.0             rtracklayer_1.46.0            xfun_0.42                    
[49] stringr_1.5.1                 mime_0.11                     lifecycle_1.0.4               XML_3.99-0.3                 
[53] zoo_1.8-9                     zlibbioc_1.32.0               scales_1.3.0                  gggrid_0.2-0                 
[57] BSgenome_1.54.0               VariantAnnotation_1.32.0      promises_1.2.0.1              hms_1.1.0                    
[61] ProtGenerics_1.18.0           SummarizedExperiment_1.16.1   RBGL_1.62.1                   LDlinkR_1.3.0                
[65] RColorBrewer_1.1-2            yaml_2.2.1                    curl_5.2.1                    memoise_2.0.1                
[69] gridExtra_2.3                 biomaRt_2.42.1                rpart_4.1.19                  latticeExtra_0.6-29          
[73] stringi_1.7.3                 RSQLite_2.3.1                 BiocVersion_3.10.1            checkmate_2.3.1              
[77] BiocParallel_1.20.1           rlang_1.1.3                   pkgconfig_2.0.3               matrixStats_0.59.0           
[81] bitops_1.0-7                  lattice_0.20-45               purrr_1.0.2                   GenomicAlignments_1.22.1     
[85] ggstats_0.5.1                 htmlwidgets_1.5.3             labeling_0.4.2                bit_4.0.4                    
[89] tidyselect_1.2.0              GGally_2.2.1                  plyr_1.8.6                    magrittr_2.0.3               
[93] R6_2.5.1                      generics_0.1.0                Hmisc_4.7-2                   DelayedArray_0.12.3          
[97] DBI_1.1.1                     pillar_1.9.0                  foreign_0.8-81                withr_3.0.0                  
[101] survival_3.5-5                RCurl_1.98-1.3                nnet_7.3-19                   tibble_3.2.1                 
[105] crayon_1.4.1                  utf8_1.2.1                    plotly_4.10.4                 OrganismDbi_1.28.0           
[109] jpeg_0.1-8.1                  progress_1.2.2                grid_3.6.3                    data.table_1.14.0            
[113] blob_1.2.1                    digest_0.6.34                 xtable_1.8-4                  httpuv_1.6.1                 
[117] tidyr_1.3.1                   openssl_2.1.1                 munsell_0.5.0                 viridisLite_0.4.0            
[121] askpass_1.1

How can I fix it? Can I get recombination rate from UCSC, and insert in the data to visualize?

Second, I'm trying to align regional plot from locuszoomr and gene model from ggbio by using cowplot. Aligning of y-axis was successful, but the ranges of x-axis didn't match. Is there any option to control xlim in ggplot version of locuszoomr?
Following codes were used to align the plots.

loc <- locus(
  data = tb,
  seqname = 5,
  xrange = c(96207000, 96259000),
  fix_window = 0,
  ens_db = "EnsDb.Hsapiens.v75"
)
p1 <- gg_scatter(loc)
p2 <- gg_genetracks(loc)
# load window
df <- read.table(
  "deletion_window.bed",
  sep = "\t",
  header = FALSE,
  stringsAsFactors = FALSE
)
bed <- sapply(
  split(df, df$V4),
  function(i) {
    GRanges(
      seqnames = i$V1,
      ranges = IRanges(
        start = i$V2,
        end = i$V3,
        names = i$V4
      )
    )
  }
)
# load gene model
txdb <- makeTxDbFromGFF(
  "gene_model.gtf",
  format = "gtf"
)
p3 <- autoplot(txdb, which = bed$gene)
plot_grid(p1, p2, p3@ggplot, ncol = 1, align = "v")

It's resulting plot.

`No genes to plot` despite genes in ens_db

Hey Myles,

its me (yet again)...
I am currently using AnnotationHub to get the latest ens_db object for GRCh38. I noticed, that for some loci, I get the message "No genes to plot". However, I know for a fact that there are genes in the region. I am also able to manually search the ens_db object and list the genes that should be plotted.
This is code to reproduce the issue:

ah <- AnnotationHub()
# this is the latest ensembl annotation
# query(ah, c("EnsDb", "v109"))
ensDB_v109 <- ah[["AH109606"]]

x <- fread("example.tsv")
chr=1
start = 247416156 - 110e3 # these are different from the coloc_susie script because we use hg38 here
stop = 247449108 + 110e3

tmp_loc <- locus(
    data =x,
    seqname = "chr1",
    chrom = "Chromosome_phe",
    xrange = c(start, stop),
    flank = 0,
    p = "Nominal_pvalue",
    pos = "Pos_variant",
    ens_db = ensDB_v109,
    labs = "gene_snp")
locus_plot(tmp_loc) # -> No genes to plot

# Manually look up the ensDB object:
genes(ensDB_v109) %>% as.data.frame() %>%
    filter(start > 247416156 - 110e3) %>%
    filter(start < 247449108 + 110e3) %>% View() # shows the genes that I expect to be in the region.

The example data can be downloaded here:
https://we.tl/t-wgfpRz9aHd

As always, any insights are much appreciated!

Cheers,
Nick

Error: near ")": syntax error

Hi Myles,

I've encountered a syntax error while using the locus function, and I'm having trouble diagnosing the problem. The error occurs when I execute the following code:

loc <- locus(data = gwas_select, seqname = chr, xrange =  range,ens_db = "EnsDb.Hsapiens.v75")
Chromosome 9, position 91453236 to 91553236
1214 SNPs/datapoints
Error: near ")": syntax error

I have reviewed the gwas_select object, and it appears to be consistent with other objects that I have successfully processed without encountering this issue. For your reference, here is the output for the chr and range variables:

> chr
[1] 9
> range
[1] 91453236 91553236

and the gwas object is gwas.txt

Could you please help me identify what might be causing this syntax error? Any insights or suggestions you could provide would be greatly appreciated.

Thank you!
Xiaotong

[Feature Request] Include Recombination Rate on secondary axis

Dear Myles,
I really fell in love with your package during the last weeks, due to the great usability, documentation and also your support! There is just one small thing, which would make this package stand out even more. And that would be the inclusion of the recombination rate in the locus zoom plot as a secondary axis. I am imaging something similar to the code from gasscoplot2 (https://github.com/jrs95/gassocplot2/blob/master/R/figures.R).

Are there any plans to implement such a functionality in the future?

Cheers!

myles-lewis / locuszoomr Goto Github PK

locuszoomr's People

Contributors

Stargazers

Watchers

Forkers

locuszoomr's Issues

Error in `check_breaks_labels()`: ! `breaks` and `labels` must have the same length

error with link_recomb

stacking gg_scatter plots on top of one another

genome build option for LD

link_recomb has curl errors

graph range in locuszoomr

`No genes to plot` despite genes in ens_db

Error: near ")": syntax error

[Feature Request] Include Recombination Rate on secondary axis

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