domino_plot: Domino Plot Visualization
In diceplot: High Dimensional Categorical Data Visualization

domino_plot

R Documentation

Domino Plot Visualization

Description

This function generates a plot to visualize gene expression levels for a given list of genes. The size of the dots can be customized, and the plot can be saved to an output file if specified.

Usage

domino_plot(
  data,
  gene_list,
  x = "gene",
  y = "Celltype",
  contrast = "Contrast",
  var_id = "var",
  log_fc = "avg_log2FC",
  p_val = "p_val_adj",
  min_dot_size = 1,
  max_dot_size = 5,
  spacing_factor = 3,
  logfc_colors = c(low = "blue", mid = "white", high = "red"),
  color_scale_name = "Log2 Fold Change",
  size_scale_name = "-log10(adj. p-value)",
  p_label_formatter = function(lp) sprintf("%.2g", 10^-lp),
  axis_text_size = 8,
  x_axis_text_size = NULL,
  y_axis_text_size = NULL,
  legend_text_size = 8,
  cluster_method = "complete",
  cluster_y_axis = TRUE,
  cluster_var_id = TRUE,
  base_width = 5,
  base_height = 4,
  show_legend = TRUE,
  legend_width = 0.25,
  legend_height = 0.5,
  custom_legend = TRUE,
  logfc_limits = NULL,
  aspect_ratio = NULL,
  switch_axis = FALSE,
  reverse_y_ordering = FALSE,
  show_var_positions = FALSE,
  output_file = NULL,
  feature_col = NULL,
  celltype_col = NULL,
  contrast_col = NULL,
  logfc_col = NULL,
  pval_col = NULL
)

Arguments

`data`	A data frame containing gene expression data.
`gene_list`	A character vector of gene names to include in the plot.
`x`	A string representing the column name in `data` for the feature variable (e.g., genes). Default is `"gene"`.
`y`	A string representing the column name in `data` for the cell type variable. Default is `"Celltype"`.
`contrast`	A string representing the column name in `data` for the contrast variable. Default is `"Contrast"`.
`var_id`	A string representing the column name in `data` for the variable identifier. Default is `"var"`.
`log_fc`	A string representing the column name in `data` for the log fold change values. Default is `"avg_log2FC"`.
`p_val`	A string representing the column name in `data` for the adjusted p-values. Default is `"p_val_adj"`.
`min_dot_size`	A numeric value indicating the minimum dot size in the plot. Default is `1`.
`max_dot_size`	A numeric value indicating the maximum dot size in the plot. Default is `5`.
`spacing_factor`	A numeric value indicating the spacing between gene pairs. Default is `3`.
`logfc_colors`	A named vector specifying the colors for the low, mid, and high values in the color scale. Default is `c(low = "blue", mid = "white", high = "red")`.
`color_scale_name`	A string specifying the name of the color scale in the legend. Default is `"Log2 Fold Change"`.
`size_scale_name`	A string specifying the name of the size scale in the legend. Default is `"-log10(adj. p-value)"`.
`p_label_formatter`	A function used to format the size legend labels (typically for p-values). Default is `function(lp) sprintf("%.2g", 10^-lp)`.
`axis_text_size`	A numeric value specifying the size of the axis text. Default is `8`.
`x_axis_text_size`	A numeric value specifying the size of the x-axis text. If NULL, uses `axis_text_size`. Default is `NULL`.
`y_axis_text_size`	A numeric value specifying the size of the y-axis text. If NULL, uses `axis_text_size`. Default is `NULL`.
`legend_text_size`	A numeric value specifying the size of the legend text. Default is `8`.
`cluster_method`	The clustering method to use. Default is `"complete"`.
`cluster_y_axis`	A logical value indicating whether to cluster the y-axis (cell types). Default is `TRUE`.
`cluster_var_id`	A logical value indicating whether to cluster the var_id. Default is `TRUE`.
`base_width`	A numeric value specifying the base width for saving the plot. Default is `5`.
`base_height`	A numeric value specifying the base height for saving the plot. Default is `4`.
`show_legend`	A logical value indicating whether to show the legend. Default is `TRUE`.
`legend_width`	A numeric value specifying the relative width of the legend. Default is `0.25`.
`legend_height`	A numeric value specifying the relative height of the legend. Default is `0.5`.
`custom_legend`	A logical value indicating whether to use a custom legend. Default is `TRUE`.
`logfc_limits`	A numeric vector of length 2 specifying the limits for the log fold change color scale. If `NULL` (default), no limits are applied.
`aspect_ratio`	A numeric value specifying the aspect ratio of the plot. If `NULL`, it's calculated automatically. Default is `NULL`.
`switch_axis`	A logical value indicating whether to switch the x and y axes. Default is `FALSE`.
`reverse_y_ordering`	A logical value indicating whether to reverse the y-axis ordering after clustering. Default is `FALSE`.
`show_var_positions`	A logical value indicating whether to show the intermediate variable positions plot. Default is `FALSE`. When `output_file` is specified with a PDF extension, both plots will be saved to a multi-page PDF if this is `TRUE`. A warning will be shown if `show_var_positions` is `TRUE` but the output file is not a PDF.
`output_file`	An optional string specifying the path to save the plot. If `NULL`, the plot is not saved. Default is `NULL`.
`feature_col`	Deprecated. Use `x` instead.
`celltype_col`	Deprecated. Use `y` instead.
`contrast_col`	Deprecated. Use `contrast` instead.
`logfc_col`	Deprecated. Use `log_fc` instead.
`pval_col`	Deprecated. Use `p_val` instead.