Last updated: 2021-07-14
Checks: 6 1
Knit directory: mistyMBC/
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library(reticulate)
library(mistyR)
library(future)
library(dplyr)
library(purrr)
library(OmnipathR)
library(stringr)
use_python("/usr/local/bin/python3")
plan(multisession)Requires python3 and anndata installed (pip install anndata).
import anndata
def read_and_extract(datapath):
adata = anndata.read(datapath)
ots = adata.obsm["OT"]
counts = adata.obsm["counts"]
geom = adata.obs[["x_orig", "y_orig"]]
markers = adata.uns["counts_var"]
return ots, counts, geom, markersGet ligand and receptor symbols from Omnipath
extract_symbols <- function(op.source) {
proteins <- op.source %>%
filter(entity_type == "protein") %>%
pull(genesymbol)
complexes <- op.source %>%
filter(entity_type == "complex") %>%
pull(genesymbol) %>%
str_remove("COMPLEX:") %>%
str_split("_") %>%
unlist()
return(union(proteins, complexes) %>% make.names())
}
op.ligands <- import_omnipath_intercell(
categories = "ligand",
secreted = TRUE,
consensus_percentile = 80
)
ligands <- extract_symbols(op.ligands)
op.receptors <- import_omnipath_intercell(
categories = "receptor",
secreted = FALSE,
consensus_percentile = 80
)
receptors <- extract_symbols(op.receptors)Define and run ligand receptor oriented mistyR pipelines for MBC cells in SlideSeq data. Relate expression of genes annotated as ligands in the neighborhood of each MBC cell to its intracellular receptor expression.
# 364 is a tricky sample
(list.files("data", ".h5ad", recursive = TRUE, full.names = TRUE) %>%
keep(~ str_detect(.x, "slide_seq")))[-4] %>%
walk(function(datapath) {
data <- py$read_and_extract(datapath)
mbs <- which(data[[1]][, which(str_detect(colnames(data[[1]]), "MBC"))] >= 0.9)
expr <- as.data.frame(as.matrix(data[[2]])) %>% slice(mbs) %>%
`colnames<-`(make.names(data[[4]]))
pos <- data[[3]] %>% slice(mbs)
unique(str_extract(rownames(pos), "-\\d$")) %>% walk(function(replicate) {
output.folder <- paste0(
str_replace(
str_remove(datapath, ".h5ad"),
"data", "output"
), replicate
)
output.folder.failed <- paste0(output.folder, "_failed")
if (!(dir.exists(output.folder) | dir.exists(output.folder.failed))) {
ind <- str_which(rownames(pos), paste0(replicate, "$"))
ligand.views <- create_initial_view(expr[ind, ] %>%
select(-names(which(apply(., 2, var) == 0))) %>%
select(any_of(ligands))) %>%
add_paraview(pos[ind, ], 100)
misty.views <- create_initial_view(expr[ind, ] %>%
select(-names(which(apply(., 2, var) == 0))) %>%
select(any_of(receptors))) %>%
add_views(list(ligand.views[["paraview.100"]]))
tryCatch(
run_misty(misty.views, results.folder = output.folder),
error = function(e) file.rename(output.folder, output.folder.failed)
)
}
})
})
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] stringr_1.4.0 OmnipathR_3.0.1 purrr_0.3.4 dplyr_1.0.7
[5] future_1.21.0 mistyR_1.1.2 reticulate_1.20 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] progress_1.2.2 tidyselect_1.1.1 xfun_0.24 bslib_0.2.5.1
[5] listenv_0.8.0 lattice_0.20-44 vctrs_0.3.8 generics_0.1.0
[9] htmltools_0.5.1.1 yaml_2.2.1 utf8_1.2.1 rlang_0.4.11
[13] jquerylib_0.1.4 later_1.2.0 pillar_1.6.1 glue_1.4.2
[17] DBI_1.1.1 rappdirs_0.3.3 readxl_1.3.1 lifecycle_1.0.0
[21] cellranger_1.1.0 codetools_0.2-18 evaluate_0.14 knitr_1.33
[25] httpuv_1.6.1 parallel_4.1.0 curl_4.3.2 fansi_0.5.0
[29] Rcpp_1.0.7 readr_1.4.0 promises_1.2.0.1 backports_1.2.1
[33] checkmate_2.0.0 jsonlite_1.7.2 parallelly_1.26.1 fs_1.5.0
[37] hms_1.1.0 png_0.1-7 digest_0.6.27 stringi_1.6.2
[41] grid_4.1.0 rprojroot_2.0.2 tools_4.1.0 magrittr_2.0.1
[45] logger_0.2.1 sass_0.4.0 tibble_3.1.2 tidyr_1.1.3
[49] crayon_1.4.1 pkgconfig_2.0.3 ellipsis_0.3.2 Matrix_1.3-4
[53] xml2_1.3.2 prettyunits_1.1.1 httr_1.4.2 assertthat_0.2.1
[57] rmarkdown_2.9 R6_2.5.0 globals_0.14.0 igraph_1.2.6
[61] git2r_0.28.0 compiler_4.1.0