Last updated: 2021-07-14
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Knit directory: mistyMBC/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 913535e | Jovan Tanevski | 2021-06-17 | Build site. |
| html | 1b68c27 | Jovan Tanevski | 2021-06-15 | Build site. |
| Rmd | 43913a8 | Jovan Tanevski | 2021-06-15 | auto publish date |
| Rmd | 34b1d9e | Jovan Tanevski | 2021-06-15 | explicit codex, merfish and exseq |
| html | e445e6f | Jovan Tanevski | 2021-06-11 | Build site. |
| Rmd | abca833 | Jovan Tanevski | 2021-06-11 | temporarily parametrize simple_misty |
| Rmd | f532a05 | Jovan Tanevski | 2021-06-10 | generalize analysis |
| html | 56bbb48 | Jovan Tanevski | 2021-06-10 | Build site. |
| Rmd | 7c0f47e | Jovan Tanevski | 2021-06-10 | wflow_publish(all = TRUE) |
| Rmd | eb056ff | Jovan Tanevski | 2021-06-10 | add simple misty analysis |
library(reticulate)
library(mistyR)
library(future)
library(purrr)
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)
counts = adata.obsm["counts"]
geom = adata.obs[["x_orig", "y_orig"]]
markers = adata.uns["counts_var"]
return counts, geom, markersDefine standard view composition and run MISTy on all h5ad files for modalities CODEX, MERFISH and ExSeq.
(list.files("data", ".h5ad", recursive = TRUE, full.names = TRUE) %>%
keep(~ str_detect(.x, "(codex|merfish|exseq)_processed"))) %>%
walk(function(datapath) {
data <- py$read_and_extract(datapath)
expr <- as.data.frame(as.matrix(data[[1]]))
colnames(expr) <- make.names(data[[3]])
pos <- data[[2]]
unique(str_extract(rownames(pos), "-\\d$")) %>% 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, "$"))
misty.views <- create_initial_view(expr[ind, ]) %>%
add_juxtaview(pos[ind, ]) %>%
add_paraview(pos[ind, ],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 purrr_0.3.4 future_1.21.0 mistyR_1.1.2
[5] reticulate_1.20 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 pillar_1.6.1 compiler_4.1.0 bslib_0.2.5.1
[5] later_1.2.0 jquerylib_0.1.4 git2r_0.28.0 tools_4.1.0
[9] digest_0.6.27 jsonlite_1.7.2 evaluate_0.14 lifecycle_1.0.0
[13] tibble_3.1.2 lattice_0.20-44 png_0.1-7 pkgconfig_2.0.3
[17] rlang_0.4.11 Matrix_1.3-4 DBI_1.1.1 parallel_4.1.0
[21] yaml_2.2.1 xfun_0.24 dplyr_1.0.7 knitr_1.33
[25] globals_0.14.0 generics_0.1.0 fs_1.5.0 vctrs_0.3.8
[29] sass_0.4.0 tidyselect_1.1.1 rprojroot_2.0.2 grid_4.1.0
[33] glue_1.4.2 listenv_0.8.0 R6_2.5.0 parallelly_1.26.1
[37] fansi_0.5.0 rmarkdown_2.9 magrittr_2.0.1 whisker_0.4
[41] codetools_0.2-18 promises_1.2.0.1 ellipsis_0.3.2 htmltools_0.5.1.1
[45] assertthat_0.2.1 httpuv_1.6.1 utf8_1.2.1 stringi_1.6.2
[49] crayon_1.4.1