DotPlot inverting colors

[dfermin]

Hello. I don't know if this is a bug or not but I was hoping to get sum clarification on this.

I have found a weird behavior in Dotplot. In my data I know that "Gene1" is highly expressed in the cells derived from treated mice vs the healthy controls ("VG1_TRT" vs "VG1_HC"). When I execute the this code:

DotPlot(ssData, features="EPHA7", group.by="subclass.l1", split.by="sampletype", dot.scale=10)  + 
theme(panel.grid.major.y=element_line(size=0.1), panel.background=element_rect(fill="seashell"))

I get the plot on the left. Since I didn't specify any colors in the DotPlot() function it should color the highest expression in blue as stated in the documentation. But it does the opposite in the case of VG1_TRT.

If I execute this code:

DotPlot(ssData, features="EPHA7", group.by="subclass.l1", split.by="sampletype", dot.scale=10, cols="Spectral")  + 
theme(panel.grid.major.y=element_line(size=0.1))

I get the DotPlot on the right correctly showing that VG1_TRT having the highest expression. As far as I can tell, if you do not specify a value for the cols argument in DotPlot the "blue is high" coloring scheme is not necessarily followed by the function as documented.

Obviously I can always ensure the correct coloring is performed by using the col="Spectral" argument to my DotPlot commands but I wasn't sure if this was a bug or not so I posted it here hoping for some suggestions.

Thanks, Damian

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.9 (Ootpa)

Matrix products: default
BLAS/LAPACK: /opt/OpenBLAS/lib/libopenblas_skylakexp-r0.3.18.so

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

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

other attached packages:
[1] RColorBrewer_1.1-3 ggpubr_0.6.0       ggplot2_3.4.2      dplyr_1.1.2        sp_1.6-0           SeuratObject_4.1.1 Seurat_4.1.1       nvimcom_0.9-115

loaded via a namespace (and not attached):
  [1] Rtsne_0.16            colorspace_2.1-0      ggsignif_0.6.4        deldir_1.0-6          ellipsis_0.3.2        ggridges_0.5.3        spatstat.data_2.2-0   farver_2.1.1          leiden_0.4.3
 [10] listenv_0.8.0         ggrepel_0.9.3         fansi_1.0.5           codetools_0.2-18      splines_4.1.2         polyclip_1.10-0       jsonlite_1.8.5        broom_0.8.0           ica_1.0-2
 [19] cluster_2.1.3         png_0.1-7             rgeos_0.6-2           uwot_0.1.14           shiny_1.7.1           sctransform_0.3.4     spatstat.sparse_2.1-1 compiler_4.1.2        httr_1.4.4
 [28] backports_1.4.1       Matrix_1.5-4          fastmap_1.1.0         lazyeval_0.2.2        cli_3.6.1             later_1.3.0           htmltools_0.5.2       tools_4.1.2           igraph_1.3.1
 [37] gtable_0.3.1          glue_1.6.2            RANN_2.6.1            reshape2_1.4.4        Rcpp_1.0.10           scattermore_0.8       carData_3.0-5         vctrs_0.6.4           nlme_3.1-157
 [46] progressr_0.11.0      lmtest_0.9-40         spatstat.random_2.2-0 stringr_1.5.0         globals_0.16.1        mime_0.12             miniUI_0.1.1.1        lifecycle_1.0.3       irlba_2.3.5
 [55] rstatix_0.7.2         goftest_1.2-3         future_1.28.0         MASS_7.3-57           zoo_1.8-11            scales_1.2.1          spatstat.core_2.4-2   promises_1.2.0.1      spatstat.utils_2.3-0
 [64] parallel_4.1.2        reticulate_1.26       pbapply_1.5-0         gridExtra_2.3         rpart_4.1.16          stringi_1.7.6         rlang_1.1.0           pkgconfig_2.0.3       matrixStats_0.62.0
 [73] lattice_0.20-45       ROCR_1.0-11           purrr_1.0.1           tensor_1.5            labeling_0.4.3        patchwork_1.1.2       htmlwidgets_1.5.4     cowplot_1.1.1         tidyselect_1.2.0
 [82] parallelly_1.32.1     RcppAnnoy_0.0.19      plyr_1.8.7            magrittr_2.0.3        R6_2.5.1              generics_0.1.3        DBI_1.1.3             pillar_1.9.0          withr_2.5.2
 [91] mgcv_1.8-40           fitdistrplus_1.1-8    survival_3.3-1        abind_1.4-5           tibble_3.2.1          future.apply_1.9.1    crayon_1.5.1          car_3.1-2             KernSmooth_2.23-20
[100] utf8_1.2.4            spatstat.geom_2.4-0   plotly_4.10.0         grid_4.1.2            data.table_1.14.2     digest_0.6.29         xtable_1.8-4          tidyr_1.3.0           httpuv_1.6.5
[109] munsell_0.5.0         viridisLite_0.4.2

[zskylarli]

Hi - have you tried DotPlot(ssData, features="EPHA7", group.by="subclass.l1", split.by="sampletype", dot.scale=10) without the additional ggplot arguments? Just wondering since we don't expect this behavior and have not seen similar bugs on our side, so this could be some sort of visualization conflict with the additional themes that you have specified. If not, please keep us updated.

[liuyu988]

i also see the same problem