hm_gpa_sel missing genes
ccshao opened this issue · 0 comments
ccshao commented
In the tutorial, when playing with the variable gene pairs, the function reported the mising genes warning. seed is 100, I am using version 0.1 (session info attached.) Could you kindly looking into it? Thanks!
hm_gpa_sel(gpTab, genes = class_info$cnProc$xpairs, grps = train, maxPerGrp = 50)
Missing genes: Ear2_Ifitm3,Ear2_Ubb,Abcg1_Ubc,Ear2_Ifitm2,Abcg1_Ubb,Abcg1_Nfkbia,Mpeg1_Ifitm3,Mpeg1_Ubb,Il18_Nfkbia,Mpeg1_Ifitm2,Sirpa_Ifitm2,Il18_Ifitm3,Il1rn_Nfkbia,Nceh1_Ubc,Il18_Jun,Klhdc4_Ubc,Il1rn_S100a6,Il1rn_Jun,Sirpa_Jun,Sirpa_Xist,Nceh1_Xist,Pla2g15_Xist,Ccl6_S100a6,Nceh1_Cd63,Pla2g15_Cd63,H2-Ob_Txn1,Cd79b_Txn1,Cd79a_Txn1,H2-Eb1_Itm2b,H2-Aa_Itm2b,H2-Ob_Ifitm3,H2-Ob_Ifitm2,H2-Oa_S100a6,H2-Oa_Ifitm3,H2-Oa_Anxa2,Cd79a_S100a6,Cd79b_Ifitm2,Cd79b_Ifitm3,H2-Eb1_Ifitm2,H2-Eb1_Anxa2,H2-Aa_Dstn,H2-Aa_S100a6,Cd37_Anxa2,Cd37_Dstn,Cd19_Dstn,H2-Ab1_Cd63,Cd19_Cd63,H2-Ab1_Cd9,Cd19_Cd9,Upk1a_Lgals1,Upk1a_Vim,Ivl_Nfkbia,Ivl_Vim,Ivl_Aldh2,Upk1b_Ifitm3,Foxq1_Hspa8,Upk1b_Ald
Warning message:
In brewer.pal(n = 12, name = "Spectral") :
n too large, allowed maximum for palette Spectral is 11
Returning the palette you asked for with that many colors
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Leap 15.2
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] singleCellNet_0.1.0 cowplot_1.1.1 reshape2_1.4.4
[4] pheatmap_1.0.12 dplyr_1.0.6 data.table_1.14.0
[7] magrittr_2.0.1 patchwork_1.1.1 ggplot2_3.3.3
[10] ll_0.1.0 colorout_1.2-2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 mvtnorm_1.1-1 lattice_0.20-41
[4] class_7.3-18 assertthat_0.2.1 digest_0.6.27
[7] utf8_1.2.1 RSpectra_0.16-0 R6_2.5.0
[10] plyr_1.8.6 rootSolve_1.8.2.1 e1071_1.7-6
[13] pillar_1.6.1 rlang_0.4.11 Exact_2.1
[16] rstudioapi_0.13 Matrix_1.3-2 reticulate_1.18
[19] labeling_0.4.2 stringr_1.4.0 munsell_0.5.0
[22] umap_0.2.7.0 proxy_0.4-25 compiler_4.0.3
[25] pkgconfig_2.0.3 askpass_1.1 DescTools_0.99.41
[28] openssl_1.4.4 tidyselect_1.1.1 tibble_3.1.2
[31] gridExtra_2.3 lmom_2.8 expm_0.999-6
[34] randomForest_4.6-14 fansi_0.5.0 viridisLite_0.4.0
[37] crayon_1.4.1 withr_2.4.2 MASS_7.3-53.1
[40] grid_4.0.3 jsonlite_1.7.2 gtable_0.3.0
[43] lifecycle_1.0.0 DBI_1.1.1 scales_1.1.1
[46] gld_2.6.2 stringi_1.6.2 farver_2.1.0
[49] viridis_0.5.1 ellipsis_0.3.2 generics_0.1.0
[52] vctrs_0.3.8 boot_1.3-27 RColorBrewer_1.1-2
[55] tools_4.0.3 glue_1.4.2 purrr_0.3.4
[58] parallel_4.0.3 colorspace_2.0-1