run_DLPFC_bayesspace.R

[noob000007]

could you please provide the datasets like in "/home/xuchang/Project/DeepST/code_20220617/All_methods/data"
because the data/DLPFC seem like can not directly run the code “dlpfc <- readVisium(dir.input) ”
thanks you very much 🙇‍

library(BayesSpace)
library(ggplot2)

data_path <- "/home/xuchang/Project/DeepST/code_20220617/All_methods/data"
save_path <- "/home/xuchang/Project/DeepST/code_20220617/All_methods/Results"

sample <- c('Section1_Posterior', 'Section1_Anterior', 'Section_Coronal', "Human_breast_FFPE")

sample <- c('151507', '151508','151509','151510', '151669', '151670', '151671', '151672', '151673','151674','151675','151676')

for (sample.name in sample ){
dir.input <- file.path(data_path, sample.name)
dir.output <- file.path(save_path, sample.name)

if(!dir.exists(file.path(dir.output))){
dir.create(file.path(dir.output), recursive = TRUE)
}

if(sample.name %in% c('151669', '151670', '151671', '151672')) {
n_clusters <- 5} else {
n_clusters <- 7}

load data

dlpfc <- readVisium(dir.input)
dlpfc <- logNormCounts(dlpfc)