Hi,

Since the Seurat update v2.4 to v3.0, when creating feature plots of gene sets i have the issue that the dots in the tsne are illustrating gene expression. Is this issue known and is there a fix?

valid.genes <- rownames(cells@assays[["RNA"]]@CountS)
IGK <- c(grep("^IGK", valid.genes, value = TRUE))
FeaturePlot(object = Data, features = IGK, ncol = 8, dims = c(1,2), cols = c("gray","red"), pt.size = 0.9, reduction = "tsne", combine = TRUE)

R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

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

other attached packages:
[1] gdata_2.18.0 ggpubr_0.2 magrittr_1.5 gtable_0.3.0
[5] gridExtra_2.3 cowplot_0.9.4 reticulate_1.12 ggplot2_3.1.1
[9] readr_1.3.1 forcats_0.4.0 dplyr_0.8.1 tibble_2.1.1
[13] Seurat_3.0.0 stringi_1.4.3

loaded via a namespace (and not attached):
[1] httr_1.4.0 tidyr_0.8.3 jsonlite_1.6
[4] viridisLite_0.3.0 splines_3.5.2 lsei_1.2-0
[7] R.utils_2.8.0 gtools_3.8.1 Rdpack_0.11-0
[10] assertthat_0.2.1 ggrepel_0.8.1 globals_0.12.4
[13] pillar_1.4.0 lattice_0.20-38 glue_1.3.1
[16] digest_0.6.18 RColorBrewer_1.1-2 SDMTools_1.1-221.1
[19] colorspace_1.4-1 htmltools_0.3.6 Matrix_1.2-15
[22] R.oo_1.22.0 plyr_1.8.4 pkgconfig_2.0.2
[25] bibtex_0.4.2 tsne_0.1-3 listenv_0.7.0
[28] purrr_0.3.2 scales_1.0.0 RANN_2.6.1
[31] Rtsne_0.15 withr_2.1.2 ROCR_1.0-7
[34] pbapply_1.4-0 lazyeval_0.2.2 survival_2.43-3
[37] crayon_1.3.4 R.methodsS3_1.7.1 future_1.13.0
[40] nlme_3.1-137 MASS_7.3-51.1 gplots_3.0.1.1
[43] ica_1.0-2 tools_3.5.2 fitdistrplus_1.0-14
[46] data.table_1.12.2 hms_0.4.2 gbRd_0.4-11
[49] stringr_1.4.0 plotly_4.9.0 munsell_0.5.0
[52] cluster_2.0.7-1 irlba_2.3.3 compiler_3.5.2
[55] rsvd_1.0.0 caTools_1.17.1.2 rlang_0.3.4
[58] ggridges_0.5.1 htmlwidgets_1.3 igraph_1.2.4.1
[61] labeling_0.3 bitops_1.0-6 npsurv_0.4-0
[64] codetools_0.2-15 reshape2_1.4.3 R6_2.4.0
[67] zoo_1.8-5 future.apply_1.2.0 KernSmooth_2.23-15
[70] metap_1.1 ape_5.3 parallel_3.5.2
[73] Rcpp_1.0.1 sctransform_0.2.0 png_0.1-7
[76] tidyselect_0.2.5 lmtest_0.9-37

I have the same issue when running the latest version of R