hm_gpa_sel missing genes

[ccshao]

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