Question: Gviz Sashimi Plot height/colour/count
gravatar for oberlins
2.5 years ago by
oberlins10 wrote:

Question: I'm trying to plot a sashimi plot of an RNA-seq experiment with Gviz. There are three thing that I would like to change in the standard layout, but I fail so far.

1. I want to reduce the height of the sashimi plot making it smaller than the coverage track. I therefore used the  "sashimiHeight" command, but it didn't work.

2. Changing the colour if the line of the sashimi plot did not work, using "col.sashimi".

3. Is there an option to display the amount of reads covering the junction on every junction event, additional to only having the line width reflecting this number?

Thanks for the help!

Here is the code I use and the plot I get:

plotTracks(c(txTr, alTrack) , chromosome = 1 ,from = 1, to =  10000, showId=TRUE, type=c("coverage","sashimi"), sashimiScore = 10, fill= "blue", col.sashimi = "red", sashimiHeight = 0.1, minSashimi=10, lwd.sashimiMax=4)

> sessionInfo()

R version 3.3.0 (2016-05-03)

Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

[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      stats4    parallel  stats     graphics  grDevices utils     datasets 
 [9] methods   base     

other attached packages:
 [1] BSgenome.Athaliana.TAIR.TAIR9_1.3.1000    BSgenome_1.40.0                          
 [3] rtracklayer_1.32.0                        Biostrings_2.40.1                        
 [5] XVector_0.12.0                            TxDb.Athaliana.BioMart.plantsmart28_3.2.2
 [7] GenomicFeatures_1.24.2                    AnnotationDbi_1.34.3                     
 [9] Gviz_1.16.1                               GenomicRanges_1.24.0                     
[11] GenomeInfoDb_1.8.1                        IRanges_2.6.0                            
[13] S4Vectors_0.10.1                          HTqPCR_1.26.0                            
[15] limma_3.28.5                              RColorBrewer_1.1-2                       
[17] ReadqPCR_1.18.0                           affy_1.50.0                              
[19] Biobase_2.32.0                            BiocGenerics_0.18.0                      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5                   biovizBase_1.20.0            
 [3] lattice_0.20-33               Rsamtools_1.24.0             
 [5] gtools_3.5.0                  digest_0.6.9                 
 [7] mime_0.4                      R6_2.1.2                     
 [9] plyr_1.8.3                    chron_2.3-47                 
[11] acepack_1.3-3.3               RSQLite_1.0.0                
[13] httr_1.1.0                    ggplot2_2.1.0                
[15] BiocInstaller_1.22.2          gplots_3.0.1                 
[17] zlibbioc_1.18.0               gdata_2.17.0                 
[19] data.table_1.9.6              rpart_4.1-10                 
[21] Matrix_1.2-6                  preprocessCore_1.34.0        
[23] splines_3.3.0                 BiocParallel_1.6.2           
[25] AnnotationHub_2.4.2           foreign_0.8-66               
[27] RCurl_1.95-4.8                biomaRt_2.28.0               
[29] munsell_0.4.3                 shiny_0.13.2                 
[31] httpuv_1.3.3                  htmltools_0.3.5              
[33] nnet_7.3-12                   SummarizedExperiment_1.2.2   
[35] gridExtra_2.2.1               interactiveDisplayBase_1.10.3
[37] Hmisc_3.17-4                  matrixStats_0.50.2           
[39] XML_3.98-1.4                  GenomicAlignments_1.8.0      
[41] bitops_1.0-6                  xtable_1.8-2                 
[43] gtable_0.2.0                  DBI_0.4-1                    
[45] scales_0.4.0                  KernSmooth_2.23-15           
[47] affyio_1.42.0                 latticeExtra_0.6-28          
[49] Formula_1.2-1                 ensembldb_1.4.3              
[51] tools_3.3.0                   dichromat_2.0-0              
[53] survival_2.39-4               colorspace_1.2-6             
[55] cluster_2.0.4                 caTools_1.17.1               
[57] VariantAnnotation_1.18.1    
ADD COMMENTlink modified 2.3 years ago by Robert Ivanek530 • written 2.5 years ago by oberlins10
gravatar for Robert Ivanek
2.3 years ago by
Robert Ivanek530
Robert Ivanek530 wrote:

Hi Stefan,

I am sorry for the delay.

1) Currently it is possible to adjust the height of "coverage" (or "sashimi") track only if also "pileup" is displayed. Otherwise each of them occupies half of the track height.

2) There was typo in the code. Thank you for pointing it out. "col.sashimi" should work in devel version 1.17.7 and release version 1.16.5

3) I added this possibility into version 1.17.7 however there is no check for resolution. You can test it with parameter sashimiNumbers=TRUE. It is still experimental.  Please let me know what do you think about it.




ADD COMMENTlink written 2.3 years ago by Robert Ivanek530
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