7 DKO chimera processing

setwd(here::here())

library("metacell")
library("tgstat")
library("tgconfig")
library("Matrix")
library("dplyr")

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

scdb_init("scrna_db/", force_reinit = T)

## initializing scdb to scrna_db/

7.0.0.1 Remove extraembryonic ectoderm and parietal endoderm cells

7.0.0.2 Merge cells with the wildtype atlas

source("scripts/pipeline/remove_exe_ectoderm_and_parietal_endo_cls.R")
source("scripts/pipeline/merge_umi_mat_with_wt10_umi_mat.R")

for (mat_nm in c("dko12_chim", "dko13_chim", "dko23_chim")) {
    print(mat_nm)
    mat <- scdb_mat(mat_nm)
    mat <- remove_exe_ectoderm_and_parietal_endoderm(mat_query = mat)
    mat_new <- merge_umi_mat_with_wt10(scmat = mat)
    scdb_add_mat(id = paste0(mat_nm, "_wt10"), mat = mat_new)
}

## [1] "dko12_chim"
## [1] "dko13_chim"
## [1] "dko23_chim"

7.0.0.3 Generate single-cell balanced kNN-graph

This step needs the file
data/tet_tko.bad_genes.txt

source("scripts/pipeline/gen_cgraph.R")

## initializing scdb to scrna_db/

gen_cgraph("dko12_chim_wt10", force_recompute_cgraph = F)

## [1] TRUE

gen_cgraph("dko13_chim_wt10", force_recompute_cgraph = F)

## [1] TRUE

gen_cgraph("dko23_chim_wt10", force_recompute_cgraph = F)

## [1] TRUE

7.0.0.4 Transfer cell type annotation to TKO cells

source("scripts/pipeline/transfer_cell_type_annotation.R")
transfer_color_chimera_tetraploid("dko12_chim_wt10")
transfer_color_chimera_tetraploid("dko13_chim_wt10")
transfer_color_chimera_tetraploid("dko23_chim_wt10")

7.0.0.5 Time chimera embryos based on their host and KO cells

source("scripts/pipeline/transfer_time_annotation.R")

## Loading required package: slam

## Loading required package: sparsesvd

source("scripts/pipeline/dko_chim_timing.R")
dko_chim_timing("dko12_chim_wt10")
dko_chim_timing("dko13_chim_wt10")
dko_chim_timing("dko23_chim_wt10")