Colour issue with autoplot

[michaeljpitcher]

Hi

I've tried to follow the vignette for ggcyto (http://bioconductor.org/packages/release/bioc/vignettes/ggcyto/inst/doc/autoplot.html) and when I use autoplot it seems as though my hexagon colours are being assigned wrong:

Code:

library(ggcyto)
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_bcell_auto",full = TRUE))
data(GvHD)
fs <- GvHD[subset(pData(GvHD), Patient %in%5 & Visit %in% c(5:6))[["name"]]]

autoplot(fs, x = 'FSC-H')
autoplot(fs, x = 'FSC-H', y = 'SSC-H', bins = 64)

Output:

SessionInfo:

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] ggcyto_1.26.0        flowWorkspace_4.10.0 ncdfFlow_2.44.0      BH_1.78.0-0         
[5] flowCore_2.10.0      ggplot2_3.4.0       

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9          plyr_1.8.8          RColorBrewer_1.1-3  pillar_1.8.1       
 [5] compiler_4.2.2      cytolib_2.10.0      tools_4.2.2         zlibbioc_1.44.0    
 [9] lattice_0.20-45     lifecycle_1.0.3     tibble_3.1.8        gtable_0.3.1       
[13] pkgconfig_2.0.3     rlang_1.0.6         graph_1.76.0        DBI_1.1.3          
[17] cli_3.4.1           rstudioapi_0.14     Rgraphviz_2.42.0    hexbin_1.28.2      
[21] gridExtra_2.3       withr_2.5.0         dplyr_1.0.10        generics_0.1.3     
[25] vctrs_0.5.1         S4Vectors_0.36.0    stats4_4.2.2        grid_4.2.2         
[29] tidyselect_1.2.0    data.table_1.14.6   glue_1.6.2          Biobase_2.58.0     
[33] R6_2.5.1            fansi_1.0.3         XML_3.99-0.12       farver_2.1.1       
[37] RProtoBufLib_2.10.0 magrittr_2.0.3      scales_1.2.1        matrixStats_0.63.0 
[41] BiocGenerics_0.44.0 assertthat_0.2.1    colorspace_2.0-3    labeling_0.4.2     
[45] utf8_1.2.2          munsell_0.5.0  

[nmahanna]

Just wanted to add I am having the same issue.

Edit:
Did some digging this morning - seems to be a ggplot error not isolated to ggcyto.

library(FamilyRank)

df = tibble(var=c(1:10000), 
            x=rbinorm(n=10000, mean1=10, mean2=20, sd1=1, sd2=2, prop=.5), 
            y=rbinorm(n=10000, mean1=20, mean2=40, sd1=5, sd2=4, prop=.5)
            )
df
ggplot(df, aes(x=x, y=y))+
  geom_hex(bins=100)+
  scale_fill_gradient(low = "blue", high = "red", na.value = NA)

[mikejiang]

I confirm this is a bug introduced by the latest ggplot 3.4
See the ticket tidyverse/ggplot2#5076