R Under development (unstable) (2024-10-04 r87208 ucrt) -- "Unsuffered Consequences"
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> 
> # Load necessary libraries
> library(diceplot)
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(ggplot2)
> library(tidyr)
> # library(diceplot) # Ensure this library is installed or remove if not needed
> 
> # Define genes
> gene_list <- c("GeneA", "GeneB", "GeneC")
> 
> # Define cell types
> cell_types <- c("Neuron", "Astrocyte", "Microglia")
> 
> # Define Contrasts
> contrasts <- c("Clinical", "Pathological")
> 
> # Define vars for each Contrast
> vars_clinical <- c("MCI-NCI", "AD-MCI", "AD-NCI")
> vars_pathological <- c("Amyloid", "Plaq N", "Tangles", "NFT")
> 
> # Create a data frame with all combinations
> data <- expand.grid(
+   gene = gene_list,
+   Celltype = cell_types,
+   Contrast = contrasts,
+   stringsAsFactors = FALSE
+ )
> 
> # Add the appropriate vars to each Contrast
> set.seed(123) # Ensure reproducibility
> data_clinical <- data %>% 
+   filter(Contrast == "Clinical") %>% 
+   mutate(var = sample(vars_clinical, n(), replace = TRUE))
> 
> data_pathological <- data %>% 
+   filter(Contrast == "Pathological") %>% 
+   mutate(var = sample(vars_pathological, n(), replace = TRUE))
> 
> # Combine the data
> data <- bind_rows(data_clinical, data_pathological)
> 
> # Assign random values for avg_log2FC and p_val_adj
> data <- data %>%
+   mutate(
+     avg_log2FC = runif(n(), min = -2, max = 2),
+     p_val_adj = runif(n(), min = 0.0001, max = 0.05)
+   )
> 
> # Use the corrected function
> p <- domino_plot(
+   data = data,
+   gene_list = gene_list,
+   switch_axis = FALSE,
+   min_dot_size = 1,
+   max_dot_size = 5,
+   output_file = "domino_plot_example.png"
+ )
Plot saved to domino_plot_example.png (7.0 x 5.0 inches)
Warning messages:
1: Removed 90 rows containing missing values or values outside the scale range
(`geom_point()`). 
2: Removed 90 rows containing missing values or values outside the scale range
(`geom_point()`). 
> 
> # Display the plot
> print(p)
Warning messages:
1: Removed 90 rows containing missing values or values outside the scale range
(`geom_point()`). 
2: Removed 90 rows containing missing values or values outside the scale range
(`geom_point()`). 
> 
> proc.time()
   user  system elapsed 
   2.26    0.53    2.81