Last updated: 2021-06-10

Checks: 6 1

Knit directory: TNBC_Multi/

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File Version Author Date Message
Rmd 7c0f47e Jovan Tanevski 2021-06-10 wflow_publish(all = TRUE)
Rmd eb056ff Jovan Tanevski 2021-06-10 add simple misty analysis

Setup

library(reticulate)
library(mistyR)
library(future)

sample <- 982
modality <- "codex"

use_python("/usr/local/bin/python3")

Extract counts and geometry

Requires python3 and anndata installed (pip install anndata).

import anndata

path_template = "data/HTAPP-{0}-SMP-7629/HTAPP-{0}-SMP-7629_{1}_processed.h5ad"
adata = anndata.read(path_template.format(int(r.sample), r.modality))
        
counts = adata.obsm["counts"]
geom = adata.obs[["x_orig", "y_orig"]]
markers = adata.uns["counts_var"]

Run misty with standard view composition

plan(multisession, workers = 6)

expr <- as.data.frame(as.matrix(py$counts))
colnames(expr) <- make.names(py$markers)
pos <- py$geom

misty.views <- create_initial_view(expr) %>%
  add_juxtaview(pos) %>%
  add_paraview(pos, 100)
Computing triangulation
Generating juxtaview
Generating paraview
run_misty(misty.views,
  results.folder = paste0("output/", sample, "_", modality)
)
Training models
Warning in ...furrr_fn(...): Negative performance detected and replaced with 0
for target CTLA4
Warning in ...furrr_fn(...): Negative performance detected and replaced with 0
for target CD69
Warning in ...furrr_fn(...): Negative performance detected and replaced with 0
for target PDPN
Warning in ...furrr_fn(...): Negative performance detected and replaced with 0
for target CD38
[1] "/Users/jovant/Work/TNBC_Multi/output/982_codex"

Plot results

misty.results <- collect_results(paste0("output/", sample, "_", modality))

Collecting improvements

Collecting contributions

Collecting importances

Aggregating
misty.results %>%
  plot_improvement_stats() %>%
  plot_view_contributions() %>%
  plot_interaction_heatmap("intra", 2) %>%
  plot_interaction_heatmap("juxta.15", 2) %>%
  plot_interaction_heatmap("para.100", 2) %>%
  plot_contrast_heatmap("intra", "juxta.15", 2) %>%
  plot_contrast_heatmap("intra", "para.100", 2)
Warning: Removed 50 rows containing missing values (geom_segment).


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] purrr_0.3.4     future_1.21.0   mistyR_1.0.2    reticulate_1.20
[5] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6         lattice_0.20-44    tidyr_1.1.3        listenv_0.8.0     
 [5] png_0.1-7          assertthat_0.2.1   rprojroot_2.0.2    digest_0.6.27     
 [9] utf8_1.2.1         parallelly_1.25.0  R6_2.5.0           evaluate_0.14     
[13] highr_0.9          ggplot2_3.3.3      pillar_1.6.1       rlang_0.4.11      
[17] whisker_0.4        furrr_0.2.2        jquerylib_0.1.4    R.utils_2.10.1    
[21] R.oo_1.24.0        Matrix_1.3-4       rmarkdown_2.8      labeling_0.4.2    
[25] readr_1.4.0        stringr_1.4.0      munsell_0.5.0      compiler_4.1.0    
[29] httpuv_1.6.1       xfun_0.23          pkgconfig_2.0.3    globals_0.14.0    
[33] htmltools_0.5.1.1  tidyselect_1.1.1   tibble_3.1.2       codetools_0.2-18  
[37] fansi_0.5.0        crayon_1.4.1       dplyr_1.0.6        later_1.2.0       
[41] R.methodsS3_1.8.1  grid_4.1.0         jsonlite_1.7.2     gtable_0.3.0      
[45] lifecycle_1.0.0    DBI_1.1.1          git2r_0.28.0       magrittr_2.0.1    
[49] scales_1.1.1       stringi_1.6.2      farver_2.1.0       fs_1.5.0          
[53] promises_1.2.0.1   bslib_0.2.5.1      ellipsis_0.3.2     generics_0.1.0    
[57] vctrs_0.3.8        RColorBrewer_1.1-2 tools_4.1.0        glue_1.4.2        
[61] hms_1.1.0          parallel_4.1.0     yaml_2.2.1         colorspace_2.0-1  
[65] knitr_1.33         sass_0.4.0