True zero on axis

[SamGG]

Hi,
How can I get a true zero on Y axis? Even if put I set -1000 as lower, no negative ticks are labelled.
Best.

library(ggcyto)
#> Loading required package: ggplot2
#> Loading required package: flowCore
#> Loading required package: ncdfFlow
#> Loading required package: RcppArmadillo
#> Loading required package: BH
#> Loading required package: flowWorkspace
data("GvHD")
fs2 <- GvHD[subset(pData(GvHD), Patient %in% 5:7 & Visit %in% c(5:6))[["name"]]]
autoplot(fs2, "Time", "FL3-H", bins = 64)  + scale_y_flowCore_fasinh(b = 1/5) + ggcyto_par_set(limits = list(x = c(0,1000), y = c(-10, 2e3)), facet = facet_wrap("name"), lab = labs_cyto("marker")) # + theme(axis.text.y=element_blank())
#> Warning: Removed 10 rows containing non-finite values (stat_binhex).
#> Warning: Removed 85 rows containing missing values (geom_hex).

sessionInfo()
#> R version 3.5.3 (2019-03-11)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 7 x64 (build 7601) Service Pack 1
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=English_United Kingdom.1252 
#> [2] LC_CTYPE=English_United Kingdom.1252   
#> [3] LC_MONETARY=English_United Kingdom.1252
#> [4] LC_NUMERIC=C                           
#> [5] LC_TIME=English_United Kingdom.1252    
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] hexbin_1.27.2             ggcyto_1.10.0            
#> [3] flowWorkspace_3.30.0      ncdfFlow_2.28.1          
#> [5] BH_1.69.0-1               RcppArmadillo_0.9.200.4.0
#> [7] flowCore_1.48.1           ggplot2_3.1.0            
#> 
#> loaded via a namespace (and not attached):
#>  [1] tidyselect_0.2.5    purrr_0.2.5         lattice_0.20-38    
#>  [4] pcaPP_1.9-73        colorspace_1.3-2    htmltools_0.3.6    
#>  [7] stats4_3.5.3        yaml_2.2.0          XML_3.98-1.16      
#> [10] rlang_0.3.4         pillar_1.4.0        glue_1.3.1         
#> [13] withr_2.1.2         Rgraphviz_2.26.0    BiocGenerics_0.28.0
#> [16] RColorBrewer_1.1-2  matrixStats_0.54.0  plyr_1.8.4         
#> [19] robustbase_0.93-3   stringr_1.3.1       zlibbioc_1.28.0    
#> [22] munsell_0.5.0       gtable_0.2.0        mvtnorm_1.0-8      
#> [25] evaluate_0.12       labeling_0.3        latticeExtra_0.6-28
#> [28] Biobase_2.42.0      knitr_1.20          parallel_3.5.3     
#> [31] DEoptimR_1.0-8      Rcpp_1.0.1          KernSmooth_2.23-15 
#> [34] corpcor_1.6.9       scales_1.0.0        backports_1.1.2    
#> [37] graph_1.60.0        IDPmisc_1.1.18      gridExtra_2.3      
#> [40] digest_0.6.18       stringi_1.2.4       dplyr_0.8.1        
#> [43] grid_3.5.3          rprojroot_1.3-2     tools_3.5.3        
#> [46] magrittr_1.5        lazyeval_0.2.1      tibble_2.1.1       
#> [49] cluster_2.0.7-1     crayon_1.3.4        rrcov_1.4-7        
#> [52] pkgconfig_2.0.2     MASS_7.3-51.1       data.table_1.11.8  
#> [55] flowViz_1.46.0      assertthat_0.2.1    rmarkdown_1.10     
#> [58] R6_2.4.0            compiler_3.5.3

^{Created on 2019-09-06 by the reprex package (v0.2.1)}

[jacobpwagner]

Hey @SamGG , could you please give me your sessionInfo() output? It will help me figure this out.

[SamGG]

Hi Jacob. Request updated. Best

[jacobpwagner]

Hi @SamGG , I'm having trouble reproducing the plot you're seeing. It seems to be giving me a true zero on the y axis. That is, this:

autoplot(fs2, "Time", "FL3-H", bins = 64) + scale_y_flowCore_fasinh(b=1/5) + ggcyto_par_set(limits=list(x=c(0,1000), y=c(-10, 2e3)), facet=facet_wrap("name"), lab=labs_cyto("marker"))

gives me this:

If I just set the y axis to a minimum of 0, it seems to do that appropriately:

autoplot(fs2, "Time", "FL3-H", bins = 64) + scale_y_flowCore_fasinh(b=1/5) + ggcyto_par_set(limits=list(x=c(0,1000), y=c(0, 2e3)), facet=facet_wrap("name"), lab=labs_cyto("marker"))

I should mention that I am using Bioconductor's 3.8 Docker image to test this, which is at R 3.5.2 and ggplot2 3.2.1, so it's possible there is a difference there that is responsible for the misrepresentation of zero. There are minor version bumps on ggcyto and flowWorkspace over what you have but I don't think they are relevant to this. My full sessionInfo() for reference:

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ggcyto_1.10.2             flowWorkspace_3.30.2     
[3] ncdfFlow_2.28.1           BH_1.69.0-1              
[5] RcppArmadillo_0.9.700.2.0 flowCore_1.48.1          
[7] ggplot2_3.2.1            

loaded via a namespace (and not attached):
 [1] pcaPP_1.9-73        Rcpp_1.0.2          plyr_1.8.4         
 [4] RColorBrewer_1.1-2  pillar_1.4.2        compiler_3.5.2     
 [7] DEoptimR_1.0-8      BiocManager_1.30.4  zlibbioc_1.28.0    
[10] tools_3.5.2         tibble_2.1.3        gtable_0.3.0       
[13] lattice_0.20-38     pkgconfig_2.0.2     rlang_0.4.0        
[16] graph_1.60.0        Rgraphviz_2.26.0    parallel_3.5.2     
[19] mvtnorm_1.0-11      hexbin_1.27.3       gridExtra_2.3      
[22] stringr_1.4.0       withr_2.1.2         dplyr_0.8.3        
[25] cluster_2.1.0       IDPmisc_1.1.19      stats4_3.5.2       
[28] grid_3.5.2          tidyselect_0.2.5    data.table_1.12.2  
[31] glue_1.3.1          robustbase_0.93-5   Biobase_2.42.0     
[34] R6_2.4.0            rrcov_1.4-7         XML_3.98-1.20      
[37] latticeExtra_0.6-28 purrr_0.3.2         corpcor_1.6.9      
[40] magrittr_1.5        scales_1.0.0        matrixStats_0.54.0 
[43] BiocGenerics_0.28.0 MASS_7.3-51.4       assertthat_0.2.1   
[46] colorspace_1.4-1    labeling_0.3        KernSmooth_2.23-15 
[49] stringi_1.4.3       flowViz_1.46.1      lazyeval_0.2.2     
[52] munsell_0.5.0       crayon_1.3.4  

As for the negative ticks, it's just not adding them because there is no data in that range. But you could always add explicit ticks if that were desired. As a side note, it looks like I am really having trouble reproducing your plots in the recent versions of the packages because the bins are not being re-evaluated appropriately during the re-scaling of the axis. The same plotting code above in the current trunk branch gives me this:

which is clearly problematic and I'll be opening an issue for that soon. I'll still loop back to figure out the discrepancy over the zero on the axis as time allows.

[SamGG]

Hi. Thanks for looking at my question, but don't waste your time on that. I am currently updating all packages on order to get an up-to-date setup with R3.5.3. I will let you about the result. I guess I will have to switch to R3.6 and to Bioc 3.9. Best

[jacobpwagner]

Sounds good, and I appreciate it. I'm actually trying to run down this scaling issue that persists in Bioc 3.9, so your post has actually been really helpful in that regard. But I think I've found the problem and I'll have it fixed soon.