library( "singleCellNet" )
class_info <- readRDS( "/home/idies/workspace/c_moor_data/singleCellNet/class_info_TM.rds" )
stPark <- utils_loadObject( "/home/idies/workspace/c_moor_data/singleCellNet/sampTab_Park_MouseKidney_062118.rda" )
stPark
sample_name <fctr> | Cluster_Number <fctr> | ||
---|---|---|---|
AAACCTGAGATATGCA.1 | AAACCTGAGATATGCA.1 | 3 | |
AAACCTGGTTGTGGCC.1 | AAACCTGGTTGTGGCC.1 | 5 | |
AAACGGGAGCGTCTAT.1 | AAACGGGAGCGTCTAT.1 | 3 | |
AAACGGGAGCTCCTTC.1 | AAACGGGAGCTCCTTC.1 | 3 | |
AAACGGGCACCTCGGA.1 | AAACGGGCACCTCGGA.1 | 3 | |
AAACGGGCAGGTGCCT.1 | AAACGGGCAGGTGCCT.1 | 5 | |
AAACGGGGTAGCTTGT.1 | AAACGGGGTAGCTTGT.1 | 3 | |
AAACGGGGTCTCAACA.1 | AAACGGGGTCTCAACA.1 | 6 | |
AAACGGGGTCTTCAAG.1 | AAACGGGGTCTTCAAG.1 | 10 | |
AAACGGGGTGACTACT.1 | AAACGGGGTGACTACT.1 | 3 |
expPark <- utils_loadObject( "/home/idies/workspace/c_moor_data/singleCellNet/expMatrix_Park_MouseKidney_Oct_12_2018.rda" )
expPark[ 1:10, 1:3 ]
10 x 3 sparse Matrix of class "dgCMatrix"
AAACCTGAGATATGCA.1 AAACCTGGTTGTGGCC.1 AAACGGGAGCGTCTAT.1
Rp1 . . .
Sox17 . . .
Mrpl15 . . .
Lypla1 . . .
Gm37988 . . .
Tcea1 . . 1
Atp6v1h . . .
Rb1cc1 1 1 .
4732440D04Rik . . .
Pcmtd1 . 1 .
nqRand = 50
crParkall<-scn_predict(class_info[['cnProc']], expPark, nrand=nqRand)
Loaded in the cnProc
All Done
sgrp = as.vector(stPark$description1)
names(sgrp) = as.vector(stPark$sample_name)
grpRand =rep("rand", nqRand)
names(grpRand) = paste("rand_", 1:nqRand, sep='')
sgrp = append(sgrp, grpRand)
# heatmap classification result
sc_hmClass(crParkall, sgrp, max=5000, isBig=TRUE, cCol=F, font=8)
stPark <- get_cate(classRes = crParkall, sampTab = stPark, dLevel = "description1", sid = "sample_name", nrand = nqRand)
Error in get_cate(classRes = crParkall, sampTab = stPark, dLevel = "description1", :
could not find function "get_cate"
sc_violinClass(sampTab = stPark, classRes = crParkall, sid = "sample_name", dLevel = "description1", addRand = nqRand)
Error in sc_violinClass(sampTab = stPark, classRes = crParkall, sid = "sample_name", :
unused argument (sid = "sample_name")
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8
Matrix products: default
BLAS: /home/idies/R/lib64/R/lib/libRblas.so
LAPACK: /home/idies/R/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_1.2-18 singleCellNet_0.1.0 cowplot_1.1.1
[4] reshape2_1.4.4 pheatmap_1.0.12 dplyr_1.0.7
[7] ggplot2_3.3.3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 plyr_1.8.6 RColorBrewer_1.1-2
[4] bslib_0.2.4 compiler_4.0.3 pillar_1.6.0
[7] jquerylib_0.1.4 tools_4.0.3 digest_0.6.27
[10] lattice_0.20-41 jsonlite_1.7.2 evaluate_0.14
[13] lifecycle_1.0.0 tibble_3.1.1 gtable_0.3.0
[16] pkgconfig_2.0.3 rlang_0.4.10 rstudioapi_0.13
[19] cli_2.5.0 DBI_1.1.1 parallel_4.0.3
[22] yaml_2.2.1 xfun_0.22 withr_2.4.2
[25] stringr_1.4.0 knitr_1.33 generics_0.1.0
[28] sass_0.3.1 vctrs_0.3.8 grid_4.0.3
[31] tidyselect_1.1.1 glue_1.4.2 R6_2.5.0
[34] fansi_0.4.2 rmarkdown_2.7 farver_2.1.0
[37] purrr_0.3.4 magrittr_2.0.1 scales_1.1.1
[40] ellipsis_0.3.2 htmltools_0.5.1.1 randomForest_4.6-14
[43] assertthat_0.2.1 colorspace_2.0-0 utf8_1.2.1
[46] stringi_1.5.3 munsell_0.5.0 crayon_1.4.1