misty
Jovan Tanevski
2021-10-28
Last updated: 2021-10-28
Checks: 7 0
Knit directory: Multispectral HCC/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 434cb0d | Jovan Tanevski | 2021-10-27 | Build site. |
| html | 668b155 | Jovan Tanevski | 2021-10-27 | Build site. |
| Rmd | e4ef937 | Jovan Tanevski | 2021-10-27 | remove beta-cat from misty, update par |
| html | 68cbc32 | Jovan Tanevski | 2021-10-08 | Build site. |
| Rmd | db035f5 | Jovan Tanevski | 2021-10-08 | add misty analysis on tumor hepatocytes |
Setup
library(mistyR)
library(future)
library(tidyverse)
library(skimr)
plan(multisession(workers = 6))data <- read_csv("data/tumor_hepatocytes.csv", col_types = cols())
tumor.hc <- data %>%
select(
`Cytoplasm AGS (Opal 690) Mean (Normalized Counts, Total Weighting)`,
`Cytoplasm BerEP4 (Opal 650) Mean (Normalized Counts, Total Weighting)`,
`Cytoplasm CRP (Opal 540) Mean (Normalized Counts, Total Weighting)`,
`Nucleus p-S6 (Opal 570) Mean (Normalized Counts, Total Weighting)`,
# `Nucleus beta-cat. (Opal 520) Mean (Normalized Counts, Total Weighting)`
) %>%
`colnames<-`(str_split(colnames(.), " ") %>%
map_chr(~ .x[2]) %>%
make.names())
skim(tumor.hc)| Name | tumor.hc |
| Number of rows | 223846 |
| Number of columns | 4 |
| _______________________ | |
| Column type frequency: | |
| numeric | 4 |
| ________________________ | |
| Group variables | None |
Variable type: numeric
| skim_variable | n_missing | complete_rate | mean | sd | p0 | p25 | p50 | p75 | p100 | hist |
|---|---|---|---|---|---|---|---|---|---|---|
| AGS | 0 | 1 | 0.27 | 0.41 | 0 | 0.07 | 0.12 | 0.25 | 5.23 | ▇▁▁▁▁ |
| BerEP4 | 0 | 1 | 1.09 | 2.19 | 0 | 0.21 | 0.32 | 0.58 | 24.08 | ▇▁▁▁▁ |
| CRP | 0 | 1 | 2.51 | 3.08 | 0 | 0.55 | 1.00 | 3.50 | 35.80 | ▇▁▁▁▁ |
| p.S6 | 0 | 1 | 1.31 | 1.25 | 0 | 0.58 | 0.94 | 1.61 | 35.24 | ▇▁▁▁▁ |
Run MISTy
data %>%
select(`Sample Name`, `Cell X Position`, `Cell Y Position`) %>%
`colnames<-`(c("Sample", "X", "Y")) %>%
bind_cols(tumor.hc) %>%
group_by(Sample) %>%
group_walk(\(subset, key){
patient <- str_extract(key %>% pull(Sample), "[0-9]+_[0-9]+")
output.folder <- paste0("output/misty/", patient)
if (file.exists(output.folder) |
file.exists(paste0(output.folder, "_failed"))) {
return()
}
expr <- subset %>%
select(-c(X, Y)) %>%
select(where(~!(sd(.x) == 0 | length(unique(.x)) < 3)))
pos <- subset %>% select(X, Y)
misty.views <- create_initial_view(expr) %>%
add_juxtaview(pos, 25) %>%
add_paraview(pos, 150, 25)
tryCatch(
run_misty(misty.views, output.folder, cv = 3),
error = function(e) {
file.rename(
output.folder,
paste0(output.folder, "_failed")
)
}
)
})Collect and browse results
misty.results <- collect_results(list.dirs("output/misty")[-1])
Collecting improvements
Collecting contributions
Collecting importances
Aggregatingmisty.results %>%
plot_improvement_stats("intra.R2") %>%
plot_improvement_stats() %>%
plot_view_contributions()
misty.results %>%
plot_interaction_heatmap("intra", 0) %>%
plot_interaction_heatmap("juxta.25", 0) %>%
plot_interaction_heatmap("para.150", 0)
Signature analysis
sig <- misty.results %>%
extract_signature("performance") %>%
mutate(sample = str_extract(sample, "[0-9]+_[0-9]+"))
sig.pca <- prcomp(sig %>% select(-sample))$x %>%
data.frame() %>%
bind_cols(sig %>% select(sample))
ggplot(sig.pca, aes(x = PC1, y = PC2, color = sample)) +
geom_point() +
theme_classic()
sessionInfo()R version 4.1.1 (2021-08-10)
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.0.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] skimr_2.1.3 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[5] purrr_0.3.4 readr_2.0.2 tidyr_1.1.4 tibble_3.1.5
[9] ggplot2_3.3.5 tidyverse_1.3.1 future_1.22.1 mistyR_1.1.14
[13] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] fs_1.5.0 lubridate_1.8.0 bit64_4.0.5 RColorBrewer_1.1-2
[5] httr_1.4.2 rprojroot_2.0.2 repr_1.1.3 tools_4.1.1
[9] backports_1.3.0 bslib_0.3.1 utf8_1.2.2 R6_2.5.1
[13] DBI_1.1.1 colorspace_2.0-2 withr_2.4.2 tidyselect_1.1.1
[17] bit_4.0.4 compiler_4.1.1 git2r_0.28.0 cli_3.0.1
[21] rvest_1.0.2 xml2_1.3.2 labeling_0.4.2 sass_0.4.0
[25] scales_1.1.1 digest_0.6.28 rmarkdown_2.11 R.utils_2.11.0
[29] base64enc_0.1-3 pkgconfig_2.0.3 htmltools_0.5.2 parallelly_1.28.1
[33] dbplyr_2.1.1 fastmap_1.1.0 highr_0.9 rlang_0.4.12
[37] readxl_1.3.1 rstudioapi_0.13 jquerylib_0.1.4 generics_0.1.1
[41] farver_2.1.0 jsonlite_1.7.2 vroom_1.5.5 R.oo_1.24.0
[45] magrittr_2.0.1 Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0
[49] lifecycle_1.0.1 R.methodsS3_1.8.1 furrr_0.2.3 stringi_1.7.5
[53] whisker_0.4 yaml_2.2.1 grid_4.1.1 parallel_4.1.1
[57] listenv_0.8.0 promises_1.2.0.1 crayon_1.4.1 haven_2.4.3
[61] hms_1.1.1 knitr_1.36 pillar_1.6.4 codetools_0.2-18
[65] reprex_2.0.1 glue_1.4.2 evaluate_0.14 modelr_0.1.8
[69] vctrs_0.3.8 tzdb_0.1.2 httpuv_1.6.3 cellranger_1.1.0
[73] gtable_0.3.0 assertthat_0.2.1 xfun_0.27 broom_0.7.9
[77] later_1.3.0 globals_0.14.0 ellipsis_0.3.2