MS lesions: Doublet identification
Will Macnair
Institute for Molecular Life Sciences, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics (SIB), University of Zurich, SwitzerlandApril 28, 2021
Last updated: 2021-04-28
Checks: 6 1
Knit directory: MS_lesions/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 21997f9 | wmacnair | 2021-02-10 | Script and code to run scDblFinder |
Setup / definitions
Libraries
Helper functions
source('code/ms02_doublet_id.R')Inputs
# dirs
date_stamp = format(Sys.Date(), '%Y_%m_%d')
## read
data_dir = 'data/sce_raw'
sce_f = file.path(data_dir, 'ms_sce.rds')Outputs
save_dir = 'output/ms02_doublet_id'
dbl_f = file.path(save_dir, 'scDblFinder_outputs.txt')
dimred_f = file.path(save_dir, 'scDblFinder_dimreds.txt')Load inputs
Processing / calculations
sc_dbl_dt = calc_sc_dbl_dt(sce_f, dbl_f)scDblFinder already done! loadingdimred_dt = calc_dimred_dt(sce_f, dimred_f)dimensionality reduction already done! loadingassert_that( all(sort(dimred_dt$cell_id) == sort(sc_dbl_dt$cell_id)) )[1] TRUEAnalysis
Checks of doublet ID calcs
Samples are shown in decreasing order of doublet proportion.
# calculate ordering of samples
lib_list = sc_dbl_dt %>%
.[, .(
prop_dbl=mean(class == 'doublet')
), by=.(library_id=sample)] %>%
setorder(-'prop_dbl') %>%
use_series('library_id')
# plot them all
for (l in lib_list) {
cat('### ', l, '\n')
print(dimred_plot(l, sc_dbl_dt, dimred_dt))
cat('\n\n')
}EU025
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Outputs
devtools::session_info()- Session info ---------------------------------------------------------------
setting value
version R version 4.0.3 (2020-10-10)
os CentOS Linux 7 (Core)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype C
tz Europe/Zurich
date 2021-04-28
- Packages -------------------------------------------------------------------
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[1] /pstore/home/macnairw/lib/conda_r3.12
[2] /pstore/home/macnairw/.conda/envs/r_4.0.3/lib/R/library
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /pstore/home/macnairw/.conda/envs/r_4.0.3/lib/libopenblasp-r0.3.12.so
locale:
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attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
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[27] workflowr_1.6.2
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