In AskExplain/GeneCodeR: Transforms between image and gene expression modalities from Spatial Transcriptomics

GeneCodeR spatial displacement to test invariance

Reload important files recently saved:

main_path <- "~/Documents/main_files/AskExplain/Q4_2022/gcode/"

# Please replace this path
path_to_save <- paste(main_path,"./temp_save_dir/",sep="")

load(file = paste(sep="",path_to_save,"all_genecoder.RData"))

Set up the test configuration for GeneCodeR

# Set up genecoder transform information
genecoder.config <- GeneCodeR::extract_config_framework(F)
genecoder.config$transform$from <- 1
genecoder.config$transform$to <- 2
genecoder.config$extract_spots$window_size <- 30

Set up validation functions to evaluate statistically significant differences via a t-test, and, cosine similarity.

# Testing functions

# cosine metric for similarity between observations

test_sample_and_genes <- function(a,b,non_zero_markers,test_type="cosine"){

  if (test_type == "t.test"){

    return(
      list(

        sample_wise = do.call('c',parallel::mclapply(c(1:dim(a)[1]),function(X){

          t.test(as.numeric(a[X,non_zero_markers[X,]]),as.numeric(b[X,non_zero_markers[X,]]))$p.value

        },mc.cores = 8)),

        gene_wise = do.call('c',parallel::mclapply(c(1:dim(a)[2]),function(X){

          t.test(as.numeric(a[non_zero_markers[,X],X]),as.numeric(b[non_zero_markers[,X],X]))$p.value

        },mc.cores = 8))

      )
    )
  } 

  if (test_type == "cosine"){
    return(
      list(

        sample_wise = do.call('c',parallel::mclapply(c(1:dim(a)[1]),function(X){

          lsa::cosine(as.numeric(a[X,non_zero_markers[X,]]),as.numeric(b[X,non_zero_markers[X,]]))

        },mc.cores = 8)),

        gene_wise = do.call('c',parallel::mclapply(c(1:dim(a)[2]),function(X){

          lsa::cosine(as.numeric(a[non_zero_markers[,X],X]),as.numeric(b[non_zero_markers[,X],X]))

        },mc.cores = 8))

      )
    )
  } 
}

Displacement testing is used to evaluate how gene levels change when the image spot is displaced from where gene expression is experimentally measured. It is expected that as the displacement increases, the gene expression difference should become weaker in terms of cosine similarity correlation. Notice that from taking gradually increasing displacements, the cosine correlation can be seen to follow a similar trend (e.g. 0 pixel displacement vs 10,20,30 pixel displacements).

# Spatial displacement testing

displace_spot2gex <- list()
for (displace_val in c(0,10,20,30)){
  genecoder.config$extract_spots$rotation <- 0
  genecoder.config$extract_spots$displacement_x <- displace_val
  genecoder.config$extract_spots$displacement_y <- displace_val

  displace_test_spot_data <- GeneCodeR::prepare_spot(file_path_list = test_file_path_list,meta_info_list = meta_info_list,config = genecoder.config, gex_data = test_gex_data$gex)

  displace_spot2gex[[as.character(displace_val)]] <- GeneCodeR::genecoder(model=genecoder.model, x = displace_test_spot_data$spot, config = genecoder.config, model_type = "gcode")
}



count <- 0
cosine.simil_scores <- c()
for (i in c(1:4)){
  for (j in c(1:4)){
    if (i>j){
      count <- count + 1
      cosine.simil_scores[[count]] <- test_sample_and_genes(a = displace_spot2gex[[i]],b = displace_spot2gex[[j]], non_zero_markers = non_zero_markers, test_type = "t.test") 
    }
  }
}

displace_spot2gex <- cosine.simil_scores

print(c("displace cosine correlation; sample-wise",paste(c("0vs10:    ","0vs20:    ","10vs20:    ","0vs30:    ","10vs30:    ","20vs30:    "),round(do.call('c',lapply(displace_spot2gex,function(X){mean(X$sample_wise)})),10))))

print(c("displace cosine correlation; gene-wise",paste(c("0vs10:    ","0vs20:    ","10vs20:    ","0vs30:    ","10vs30:    ","20vs30:    "),round(do.call('c',lapply(displace_spot2gex,function(X){mean(X$gene_wise)})),10))))


rm(list=ls())
gc()

AskExplain/GeneCodeR documentation built on Jan. 3, 2023, 3:52 a.m.