Hi,

Some of Gviz display pars work but some others don't work. Is this a bug?

Example 1:

atrack <- AnnotationTrack(GRanges, name = "ORF", shape = "arrow", 
                  id = ORF$gene,  featureAnnotation  =  "id", 
                  showFeatureId = TRUE,rotation=60)

rotation=0: Numeric scalar. The degree of text rotation for item identifiers.

rotation.title=90: 

While changed rotation.title to 60, title text changed accordingly. However, change rotation to 60, no changes were oberseved for AnnotationId text, i.e. id.

Update: set rotation.item=60 will do what I want. Don't know rotation's role.

Example 2:

e <- makeGRangesFromDataFrame(ORF_expression,keep.extra.columns = TRUE)
strand(e) <- "*"
names(e) <- e$feature
dtrack6 <- DataTrack(e, name="MicroArray")
displayPars(dtrack6) <- list(type="heatmap", ylim=c(-7,8),
                             showSampleNames=TRUE, gradient=c("blue","white","red"),ncolor=100)

By set ylim, I want to fix the heatmap scale. For example, set -7 to blue, white to 0, and 8 to red. But it doesn't work, heatmap bar change one by one, as according to the values in the corresponding panels. By contrast, changing values of gradient and/or ncolor make graph different.

Am I wrong in using these pars or it is a bug?

Thanks.

sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
 [1] scales_0.2.4         Rsamtools_1.20.2     ggplot2_1.0.1        ChIPpeakAnno_3.2.2   RSQLite_1.0.0       
 [6] DBI_0.3.1            Biostrings_2.36.1    XVector_0.8.0        biomaRt_2.24.0       VennDiagram_1.6.9   
[11] Gviz_1.12.0          GenomicRanges_1.20.3 GenomeInfoDb_1.4.0   IRanges_2.2.1        S4Vectors_0.6.0     
[16] BiocGenerics_0.14.0 

loaded via a namespace (and not attached):
 [1] VariantAnnotation_1.14.1 reshape2_1.4.1           splines_3.2.0            lattice_0.20-31         
 [5] colorspace_1.2-6         rtracklayer_1.28.3       GenomicFeatures_1.20.1   RBGL_1.44.0             
 [9] XML_3.98-1.1             survival_2.38-1          foreign_0.8-63           BiocParallel_1.2.2      
[13] RColorBrewer_1.1-2       lambda.r_1.1.7           matrixStats_0.14.0       plyr_1.8.2              
[17] stringr_1.0.0            zlibbioc_1.14.0          munsell_0.4.2            gtable_0.1.2            
[21] futile.logger_1.4.1      latticeExtra_0.6-26      Biobase_2.28.0           BiocInstaller_1.18.2    
[25] AnnotationDbi_1.30.1     proto_0.3-10             Rcpp_0.11.6              acepack_1.3-3.3         
[29] BSgenome_1.36.0          limma_3.24.5             graph_1.46.0             Hmisc_3.16-0            
[33] gridExtra_0.9.1          digest_0.6.8             stringi_0.4-1            biovizBase_1.16.0       
[37] tools_3.2.0              bitops_1.0-6             magrittr_1.5             RCurl_1.95-4.6          
[41] dichromat_2.0-0          Formula_1.2-1            cluster_2.0.1            futile.options_1.0.0    
[45] GO.db_3.1.2              MASS_7.3-40              rpart_4.1-9              GenomicAlignments_1.4.1 
[49] nnet_7.3-9               multtest_2.24.0