Last updated: 2022-10-18
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Knit directory: synovialscrnaseq/
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/scRNAseq_complete_00-1_swappedDrops.Rmd
) and HTML (public/scRNAseq_complete_00-1_swappedDrops.html
) files. If you’ve configured a remote Git repository (see ?wflow_git_remote
), click on the hyperlinks in the table below to view the files as they were in that past version.
File | Version | Author | Date | Message |
---|---|---|---|---|
html | 3443cc6 | Reto Gerber | 2022-04-25 | Update |
html | f2e34e1 | Reto Gerber | 2021-07-29 | Update navbar |
html | 222b0d1 | Reto Gerber | 2021-07-29 | Update analysis to v5 |
Rmd | e88c23e | Reto Gerber | 2021-07-12 | add ambient RNA analysis |
html | e88c23e | Reto Gerber | 2021-07-12 | add ambient RNA analysis |
Rmd | 3072789 | Reto Gerber | 2021-06-09 | Update annotation scripts |
html | 3072789 | Reto Gerber | 2021-06-09 | Update annotation scripts |
suppressPackageStartupMessages({
library(dplyr)
library(ggplot2)
library(purrr)
library(stringr)
library(scater)
library(scran)
library(scuttle)
library(tidySingleCellExperiment)
library(DropletUtils)
})
n_workers <- 20
RhpcBLASctl::blas_set_num_threads(n_workers)
# bp_param <- BiocParallel::MulticoreParam(workers=20)
here::here()
[1] "/home/retger/Synovial/synovialscrnaseq"
raw_data_dir <- here::here("..","data_server")
raw_data_dir_blaz <- here::here("..","data_blaz")
remove_low_quality_samples <- TRUE
set.seed(100)
metadata_df <- readRDS(here::here("output","Sample_summaries_direct_dissociation.rds"))
order_id <- "24300"
# for order 24300
samples <- here::here(raw_data_dir,list.files(raw_data_dir),"molecule_info.h5")
names(samples) <- purrr::map_chr(strsplit(samples, "/") , ~ .x[length(.x)-1])
samples <- samples[names(samples) %in% metadata_df$`FGCZ_Sample Name`[metadata_df$Order_FGCZ == order_id]]
samples_blaz_names <- c("o24300_1_08-akg1_BB","o24300_1_09-control2_MFB","o24300_1_10-akg2_MFB","o24300_1_13-control1_BB")
samples_blaz <- here::here(raw_data_dir_blaz, samples_blaz_names,"molecule_info.h5")
names(samples_blaz) <- samples_blaz_names
samples <- c(samples, samples_blaz)
# subset for testing
# samples <- samples[c(3,10)]
before.stats <- BiocParallel::bplapply(BPPARAM = BiocParallel::MulticoreParam(workers=n_workers, RNGseed = 123),
samples, get10xMolInfoStats)
saveRDS(before.stats, here::here("output",paste0("syn_v4_swappedDrops_",order_id,"_before.rds")))
max.umi <- vapply(before.stats, function(x) max(x$num.umis), 0)
ylim <- c(1, max(max.umi))
max.ncells <- vapply(before.stats, nrow, 0L)
xlim <- c(1, max(max.ncells))
plot(0,0,type="n", xlab="Rank", ylab="Number of UMIs",
log="xy", xlim=xlim, ylim=ylim)
Warning in xy.coords(x, y, xlabel, ylabel, log): 1 x value <= 0 omitted from
logarithmic plot
Warning in xy.coords(x, y, xlabel, ylabel, log): 1 y value <= 0 omitted from
logarithmic plot
for (i in seq_along(before.stats)) {
u <- sort(before.stats[[i]]$num.umis, decreasing=TRUE)
lines(seq_along(u), u, col=i, lwd=5)
}
legend("topright", col=seq_along(before.stats),
lwd=5, legend=stringr::str_split(names(before.stats),"-",simplify = TRUE)[,2])
Version | Author | Date |
---|---|---|
3072789 | Reto Gerber | 2021-06-09 |
after.mat <- swappedDrops(samples,get.swapped=TRUE,get.diagnostics=TRUE)
saveRDS(after.mat, here::here("output",paste0("syn_v4_swappedDrops_",order_id,"_after.rds")))
cleaned.sum <- vapply(after.mat$cleaned, sum, 0)
swapped.sum <- vapply(after.mat$swapped, sum, 0)
swapped.sum / (swapped.sum + cleaned.sum)
o24300_1_01-79 o24300_1_02-86 o24300_1_03-83
0.02998419 0.02336929 0.03091428
o24300_1_04-84 o24300_1_05-78 o24300_1_06-81
0.03072419 0.08318399 0.03363505
o24300_1_07-87 o24300_1_11-80 o24300_1_12-89
0.05538205 0.04705487 0.07608163
o24300_1_08-akg1_BB o24300_1_09-control2_MFB o24300_1_10-akg2_MFB
0.03899989 0.03400100 0.03435084
o24300_1_13-control1_BB
0.09283039
plot(0,0,type="n", xlab="Rank", ylab="Number of UMIs",
log="xy", xlim=xlim, ylim=ylim)
Warning in xy.coords(x, y, xlabel, ylabel, log): 1 x value <= 0 omitted from
logarithmic plot
Warning in xy.coords(x, y, xlabel, ylabel, log): 1 y value <= 0 omitted from
logarithmic plot
for (i in seq_along(after.mat$cleaned)) {
cur.stats <- barcodeRanks(after.mat$cleaned[[i]])
u <- sort(cur.stats$total, decreasing=TRUE)
lines(seq_along(u), u, col=i, lwd=5)
}
Warning in smooth.spline(x[new.keep], y[new.keep], df = df, ...): not using
invalid df; must have 1 < df <= n := #{unique x} = 17
legend("topright", col=seq_along(after.mat$cleaned),
lwd=5, legend=stringr::str_split(names(after.mat$cleaned),"-",simplify = TRUE)[,2])
Version | Author | Date |
---|---|---|
3072789 | Reto Gerber | 2021-06-09 |
order_id <- "24793"
# for order 24793
samples <- here::here(raw_data_dir,list.files(raw_data_dir),"molecule_info.h5")
names(samples) <- purrr::map_chr(strsplit(samples, "/") , ~ .x[length(.x)-1])
samples <- samples[names(samples) %in% metadata_df$`FGCZ_Sample Name`[metadata_df$Order_FGCZ == order_id]]
samples_blaz_names <- c("o24793_1_09-BB_skin_control","o24793_1_10-BB_skin_akg","o24793_1_11-BB","o24793_1_12-BB")
samples_blaz <- here::here(raw_data_dir_blaz, samples_blaz_names,"molecule_info.h5")
names(samples_blaz) <- samples_blaz_names
samples <- c(samples, samples_blaz)
# subset for testing
samples <- samples[c(1:10)]
before.stats <- BiocParallel::bplapply(BPPARAM = BiocParallel::MulticoreParam(workers=n_workers, RNGseed = 123),
samples, get10xMolInfoStats)
saveRDS(before.stats, here::here("output",paste0("syn_v4_swappedDrops_",order_id,"_before.rds")))
max.umi <- vapply(before.stats, function(x) max(x$num.umis), 0)
ylim <- c(1, max(max.umi))
max.ncells <- vapply(before.stats, nrow, 0L)
xlim <- c(1, max(max.ncells))
plot(0,0,type="n", xlab="Rank", ylab="Number of UMIs",
log="xy", xlim=xlim, ylim=ylim)
Warning in xy.coords(x, y, xlabel, ylabel, log): 1 x value <= 0 omitted from
logarithmic plot
Warning in xy.coords(x, y, xlabel, ylabel, log): 1 y value <= 0 omitted from
logarithmic plot
for (i in seq_along(before.stats)) {
u <- sort(before.stats[[i]]$num.umis, decreasing=TRUE)
lines(seq_along(u), u, col=i, lwd=5)
}
legend("topright", col=seq_along(before.stats),
lwd=5, legend=stringr::str_split(names(before.stats),"-",simplify = TRUE)[,2])
Version | Author | Date |
---|---|---|
e88c23e | Reto Gerber | 2021-07-12 |
after.mat <- swappedDrops(samples,get.swapped=TRUE,get.diagnostics=TRUE)
saveRDS(after.mat, here::here("output",paste0("syn_v4_swappedDrops_",order_id,"_after.rds")))
cleaned.sum <- vapply(after.mat$cleaned, sum, 0)
swapped.sum <- vapply(after.mat$swapped, sum, 0)
swapped.sum / (swapped.sum + cleaned.sum)
o24793_1_01-91 o24793_1_02-92
0.011251514 0.009949212
o24793_1_03-93 o24793_1_04-95
0.012013213 0.017716810
o24793_1_05-96 o24793_1_06-98a
0.011379293 0.012042140
o24793_1_07-98b o24793_1_08-99
0.014001739 0.010291177
o24793_1_09-BB_skin_control o24793_1_10-BB_skin_akg
0.013301817 0.052566037
plot(0,0,type="n", xlab="Rank", ylab="Number of UMIs",
log="xy", xlim=xlim, ylim=ylim)
Warning in xy.coords(x, y, xlabel, ylabel, log): 1 x value <= 0 omitted from
logarithmic plot
Warning in xy.coords(x, y, xlabel, ylabel, log): 1 y value <= 0 omitted from
logarithmic plot
for (i in seq_along(after.mat$cleaned)) {
cur.stats <- barcodeRanks(after.mat$cleaned[[i]])
u <- sort(cur.stats$total, decreasing=TRUE)
lines(seq_along(u), u, col=i, lwd=5)
}
legend("topright", col=seq_along(after.mat$cleaned),
lwd=5, legend=stringr::str_split(names(after.mat$cleaned),"-",simplify = TRUE)[,2])
Version | Author | Date |
---|---|---|
e88c23e | Reto Gerber | 2021-07-12 |
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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=C
[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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] gdtools_0.2.3 DropletUtils_1.10.3
[3] tidySingleCellExperiment_1.0.0 scuttle_1.0.4
[5] scran_1.18.7 scater_1.18.6
[7] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
[9] Biobase_2.50.0 GenomicRanges_1.42.0
[11] GenomeInfoDb_1.26.7 IRanges_2.24.1
[13] S4Vectors_0.28.1 BiocGenerics_0.36.1
[15] MatrixGenerics_1.2.1 matrixStats_0.58.0
[17] stringr_1.4.0 purrr_0.3.4
[19] ggplot2_3.3.3 dplyr_1.0.4
[21] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] bitops_1.0-6 fs_1.5.0
[3] httr_1.4.2 rprojroot_2.0.2
[5] tools_4.0.3 R6_2.5.0
[7] irlba_2.3.3 HDF5Array_1.18.1
[9] vipor_0.4.5 lazyeval_0.2.2
[11] DBI_1.1.1 colorspace_2.0-0
[13] rhdf5filters_1.2.1 withr_2.4.1
[15] tidyselect_1.1.0 gridExtra_2.3
[17] compiler_4.0.3 git2r_0.28.0
[19] cli_2.3.0 BiocNeighbors_1.8.2
[21] DelayedArray_0.16.3 plotly_4.9.3
[23] scales_1.1.1 systemfonts_1.0.1
[25] digest_0.6.27 svglite_1.2.3.2
[27] R.utils_2.10.1 rmarkdown_2.6
[29] RhpcBLASctl_0.20-137 XVector_0.30.0
[31] pkgconfig_2.0.3 htmltools_0.5.1.1
[33] sparseMatrixStats_1.2.1 highr_0.8
[35] limma_3.46.0 htmlwidgets_1.5.3
[37] rlang_0.4.10 DelayedMatrixStats_1.12.3
[39] generics_0.1.0 jsonlite_1.7.2
[41] BiocParallel_1.24.1 R.oo_1.24.0
[43] RCurl_1.98-1.2 magrittr_2.0.1
[45] BiocSingular_1.6.0 GenomeInfoDbData_1.2.4
[47] Matrix_1.3-2 Rhdf5lib_1.12.1
[49] Rcpp_1.0.6 ggbeeswarm_0.6.0
[51] munsell_0.5.0 fansi_0.4.2
[53] viridis_0.5.1 R.methodsS3_1.8.1
[55] lifecycle_1.0.0 stringi_1.5.3
[57] whisker_0.4 yaml_2.2.1
[59] edgeR_3.32.1 zlibbioc_1.36.0
[61] rhdf5_2.34.0 grid_4.0.3
[63] promises_1.2.0.1 dqrng_0.2.1
[65] crayon_1.4.1 lattice_0.20-41
[67] beachmat_2.6.4 locfit_1.5-9.4
[69] knitr_1.31 pillar_1.4.7
[71] igraph_1.2.6 glue_1.4.2
[73] evaluate_0.14 data.table_1.13.6
[75] vctrs_0.3.6 httpuv_1.5.5
[77] tidyr_1.1.2 gtable_0.3.0
[79] assertthat_0.2.1 xfun_0.21
[81] rsvd_1.0.3 later_1.1.0.1
[83] viridisLite_0.3.0 tibble_3.0.6
[85] beeswarm_0.2.3 bluster_1.0.0
[87] statmod_1.4.35 ellipsis_0.3.1
[89] here_1.0.1