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Question: Gviz Sashimi Plot height/colour/count
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gravatar for oberlins
18 months ago by
oberlins10
Switzerland
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)

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      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 14 months ago by Robert Ivanek350 • written 18 months ago by oberlins10
0
gravatar for Robert Ivanek
14 months ago by
Robert Ivanek350
Switzerland
Robert Ivanek350 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.

Best

Robert

 

ADD COMMENTlink written 14 months ago by Robert Ivanek350
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