Question

TrackViewer Vignette Err: attr must be a slot name of xscale object

0

Entering edit mode

liruiradiant • 0

@liruiradiant-8906

Last seen 2.8 years ago

United States

Hello,

When I add the following command to my trackViewer Vignette:

setTrackXscaleParam(trackList[[1]], attr="position", 
                    value=list(x=122929700, y=3, label=200))

R gives me the following error:

Error in setTrackXscaleParam(trackList[[1]], attr = "position", value = list(x = 122929700, : attr must be a slot name of xscale object
3.
stop("attr must be a slot name of xscale object")
2.
setTrackXscaleParam(trackList[[1]], attr = "position", value = list(x = 122929700, y = 3, label = 200))
1.
setTrackXscaleParam(trackList[[1]], attr = "position", value = list(x = 122929700, y = 3, label = 200))

Is there something that I did wrong? Thanks!

I'll post sessionInfo() and my code below.

trackViewer • 951 views

ADD COMMENT • link 4.9 years ago liruiradiant • 0

0

Entering edit mode

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] org.Hs.eg.db_3.10.0                     TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [3] GenomicFeatures_1.38.0                  AnnotationDbi_1.48.0                   
 [5] Biobase_2.46.0                          rtracklayer_1.46.0                     
 [7] Gviz_1.30.0                             trackViewer_1.22.0                     
 [9] GenomicRanges_1.38.0                    GenomeInfoDb_1.22.0                    
[11] IRanges_2.20.1                          S4Vectors_0.24.1                       
[13] BiocGenerics_0.32.0                    

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.18.0         bitops_1.0-6                matrixStats_0.55.0          bit64_0.9-7                
 [5] RColorBrewer_1.1-2          progress_1.2.2              httr_1.4.1                  InteractionSet_1.14.0      
 [9] Rgraphviz_2.30.0            tools_3.6.1                 backports_1.1.5             R6_2.4.1                   
[13] rpart_4.1-15                Hmisc_4.3-0                 DBI_1.1.0                   lazyeval_0.2.2             
[17] colorspace_1.4-1            nnet_7.3-12                 tidyselect_0.2.5            gridExtra_2.3              
[21] prettyunits_1.0.2           bit_1.1-14                  curl_4.3                    compiler_3.6.1             
[25] graph_1.64.0                htmlTable_1.13.3            grImport_0.9-3              DelayedArray_0.12.0        
[29] scales_1.1.0                checkmate_1.9.4             stringr_1.4.0               digest_0.6.23              
[33] Rsamtools_2.2.1             foreign_0.8-72              rmarkdown_2.0               XVector_0.26.0             
[37] base64enc_0.1-3             dichromat_2.0-0             pkgconfig_2.0.3             htmltools_0.4.0            
[41] plotrix_3.7-7               ensembldb_2.10.2            BSgenome_1.54.0             htmlwidgets_1.5.1          
[45] rlang_0.4.2                 rstudioapi_0.10             RSQLite_2.1.4               BiocParallel_1.20.0        
[49] acepack_1.4.1               dplyr_0.8.3                 VariantAnnotation_1.32.0    RCurl_1.95-4.12            
[53] magrittr_1.5                GenomeInfoDbData_1.2.2      Formula_1.2-3               Matrix_1.2-18              
[57] Rcpp_1.0.3                  munsell_0.5.0               lifecycle_0.1.0             yaml_2.2.0                 
[61] stringi_1.4.3               SummarizedExperiment_1.16.0 zlibbioc_1.32.0             blob_1.2.0                 
[65] crayon_1.3.4                lattice_0.20-38             Biostrings_2.54.0           splines_3.6.1              
[69] hms_0.5.2                   zeallot_0.1.0               knitr_1.26                  pillar_1.4.2               
[73] biomaRt_2.42.0              XML_3.98-1.20               glue_1.3.1                  evaluate_0.14              
[77] biovizBase_1.34.1           latticeExtra_0.6-28         BiocManager_1.30.10         data.table_1.12.8          
[81] vctrs_0.2.0                 gtable_0.3.0                purrr_0.3.3                 assertthat_0.2.1           
[85] ggplot2_3.2.1               xfun_0.11                   AnnotationFilter_1.10.0     survival_3.1-8             
[89] tibble_2.1.3                GenomicAlignments_1.22.1    memoise_1.1.0               cluster_2.1.0

ADD REPLY • link 4.9 years ago liruiradiant • 0

0

Entering edit mode

---
title: "test"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```



```{r }
library(trackViewer)
extdata <- system.file("extdata", package="trackViewer",
                       mustWork=TRUE)
repA <- importScore(file.path(extdata, "cpsf160.repA_-.wig"),
                    file.path(extdata, "cpsf160.repA_+.wig"),
                    format="WIG")
## Because the wig file does not contain any strand info, 
## we need to set it manually.
strand(repA$dat) <- "-"
strand(repA$dat2) <- "+"


fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED",
                    ranges=GRanges("chr11", IRanges(122929000, 122931000)))
dat <- coverageGR(fox2$dat)
## We can split the data by strand into two different track channels
## Here, we set the dat2 slot to save the negative strand info. 

fox2$dat <- dat[strand(dat)=="+"]
fox2$dat2 <- dat[strand(dat)=="-"]


library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
gr <- GRanges("chr11", IRanges(122929275, 122930122), strand="-")
trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                         org.Hs.eg.db,
                         gr=gr)

```


```{r}
optSty <- optimizeStyle(trackList(repA, fox2, trs))
trackList <- optSty$tracks
viewerStyle <- optSty$style

setTrackViewerStyleParam(viewerStyle, "xaxis", FALSE)
setTrackViewerStyleParam(viewerStyle, "margin", c(.01, .05, .01, .01))
setTrackXscaleParam(trackList[[1]], "draw", TRUE)
setTrackXscaleParam(trackList[[1]], "gp", list(cex=0.8))

setTrackXscaleParam(trackList[[1]], attr="position", 
                    value=list(x=122929700, y=3, label=200))
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)
```

ADD REPLY • link 4.9 years ago liruiradiant • 0

0

Entering edit mode

Hi Iiruiradiant,

Thank you for reporting this. Could you try following code to see if there is any issue with your installation:

showMethods("setTrackXscaleParam", includeDefs = TRUE)

And also try


---
title: "test"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

```{r }
library(trackViewer)
sessionInfo()

To see if there is any difference when you compile the Rmd file.

Jianhong.

ADD REPLY • link 4.9 years ago Ou, Jianhong ★ 1.3k