[BioC] restoring lattice-like format in flowViz?

David Ornelles [guest] guest at bioconductor.org
Fri Jan 24 05:07:47 CET 2014


Is it possible to return the older "lattice" style graphics under the recent releases of FlowCore? After installing R 3.0.2 and what I could of the FlowCore packages on a new computer, I see that the default graphic output resembles something from ggplot2. (I know lattice well and ggplot not at all.) Frustratingly, this undermines much of the code I had developed to extract and further process images from various workflows. I'm afraid I am at loss of what to do short of rolling back to an earlier versions. Many thanks!

 -- output of sessionInfo(): 

Broken session (new format):
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] flowViz_1.26.15      lattice_0.20-24      flowCore_1.28.20    
[4] MASS_7.3-29          BiocInstaller_1.12.0

loaded via a namespace (and not attached):
 [1] Biobase_2.22.0      BiocGenerics_0.8.0  corpcor_1.6.6      
 [4] feature_1.2.10      graph_1.40.1        grid_3.0.2         
 [7] hexbin_1.26.3       IDPmisc_1.1.17      KernSmooth_2.23-10 
[10] ks_1.8.13           latticeExtra_0.6-26 mvtnorm_0.9-9997   
[13] parallel_3.0.2      pcaPP_1.9-49        RColorBrewer_1.0-5 
[16] robustbase_0.9-10   rrcov_1.3-4         stats4_3.0.2       
[19] tools_3.0.2

Good session (old format):
R version 2.14.2 (2012-02-29)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] flowViz_1.18.0        lattice_0.20-0        flowStats_1.12.0     
 [4] cluster_1.14.2        mvoutlier_1.9.4       robCompositions_1.5.0
 [7] car_2.0-12            nnet_7.3-1            compositions_1.10-2  
[10] energy_1.4-0          boot_1.3-4            tensorA_0.36         
[13] rgl_0.92.798          fda_2.2.7             zoo_1.7-7            
[16] flowCore_1.20.0       rrcov_1.3-01          pcaPP_1.9-45         
[19] mvtnorm_0.9-9992      robustbase_0.8-1-1    Biobase_2.14.0       
[22] MASS_7.3-17          

loaded via a namespace (and not attached):
[1] feature_1.2.8       graph_1.32.0        grid_2.14.2        
[4] KernSmooth_2.23-7   ks_1.8.6            latticeExtra_0.6-19
[7] RColorBrewer_1.0-5  stats4_2.14.2       tools_2.14.2

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