R/Figures_CannedSim.R

In eisascience/scCustFx: single-cell custom fxs Package

library(ggplot2)
library(cowplot)
library(reshape2)

# Create example data
set.seed(123)
n <- 100
L1 <- matrix(runif(n*n), nrow = n)


# Convert matrices to data frames for ggplot
L1_df <- melt(L1)
colnames(L1_df) <- c("x", "y", "value")
# Plot L1
ggplot(L1_df, aes(x = x, y = y, fill = value)) + 
  geom_tile() + 
  scale_fill_gradient(low = "blue", high = "white") + 
  ggtitle("L1") +
  theme_minimal() +
  theme(axis.title = element_blank(), axis.text = element_blank(), axis.ticks = element_blank())






Receptor_Lingand_Sim <- function(save_path = NULL, width = 12, height = 5){
  # Load required libraries
  library(ggplot2)
  library(cowplot)
  library(reshape2)
  
  # Set dimensions and parameters
  n <- 100
  circle_radius <- 10
  donut_inner_radius <- 15
  donut_outer_radius <- 20
  circle1_center <- c(75, 75)
  circle2_center <- c(25, 25)
  
  # Generate random background
  background <- matrix(runif(n*n), nrow = n)
  
  # Function to create circles
  create_circle <- function(center, radius, n) {
    circle <- matrix(0, nrow = n, ncol = n)
    for (i in 1:n) {
      for (j in 1:n) {
        if ((i - center[1])^2 + (j - center[2])^2 <= radius^2) {
          circle[i, j] <- 1
        }
      }
    }
    return(circle)
  }
  
  # Create circles for L1
  circle1 <- create_circle(circle1_center, circle_radius, n)
  circle2 <- create_circle(circle2_center, circle_radius, n)
  L1 <- background
  L1[circle1 == 1 | circle2 == 1] <- 1
  
  # Function to create donuts
  create_donut <- function(center, inner_radius, outer_radius, n) {
    donut <- matrix(0, nrow = n, ncol = n)
    for (i in 1:n) {
      for (j in 1:n) {
        dist_squared <- (i - center[1])^2 + (j - center[2])^2
        if (dist_squared <= outer_radius^2 && dist_squared >= inner_radius^2) {
          donut[i, j] <- 1
        }
      }
    }
    return(donut)
  }
  
  # Create donuts for R
  donut1 <- create_donut(circle1_center, donut_inner_radius, donut_outer_radius, n)
  donut2 <- create_donut(circle2_center, donut_inner_radius, donut_outer_radius, n)
  R <- background
  R[donut1 == 1 | donut2 == 1] <- 1
  
  # Compute difference L1-R
  diff <- L1 - R
  
  # Convert matrices to data frames for ggplot
  L1_df <- melt(L1)
  colnames(L1_df) <- c("x", "y", "value")
  R_df <- melt(R)
  colnames(R_df) <- c("x", "y", "value")
  diff_df <- melt(diff)
  colnames(diff_df) <- c("x", "y", "value")
  
  # Plot L1
  p1 <- ggplot(L1_df, aes(x = x, y = y, fill = value)) + 
    geom_tile() + 
    scale_fill_gradient(low = "blue", high = "green") + 
    theme_nothing()

  
  p1
  
  # Plot R
  p2 <- ggplot(R_df, aes(x = x, y = y, fill = value)) + 
    geom_tile() + 
    scale_fill_gradient(low = "blue", high = "green") + 
    theme_nothing()

  
  # p2
  
  # Plot L1-R
  p3 <- ggplot(diff_df, aes(x = x, y = y, fill = value)) + 
    geom_tile() + 
    scale_fill_gradient2(low = "blue", mid = "white", high = "red", midpoint = 0) + 
    ggtitle("L1-R") +
    theme_minimal() +
    theme_nothing()
  
  # p3
  
  # Arrange plots
  final_plot <- plot_grid(p1, p2, p3, nrow = 1)
  
  print(final_plot)
  
  # Save plot
  if(!is.null(save_path)) ggsave(save_path, final_plot, width = width, height = height) 
}

Receptor_Lingand_Sim(save_path = "./Receptor_Ligand_sim_pdf.pdf")