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plot_degs

Plots differentially expressed genes (DEGs) on a cell state graph, with customizable appearance and layout options.

plot_degs(
  cell_state_graph,
  deg_table,
  perturb_table = NULL,
  facet_group = "term",
  arrow_unit = 7,
  node_size = 1,
  con_colour = "darkgrey",
  fract_expr = 0.0,
  mean_expr = 0.0,
  legend_position = "none",
  fc_limits = c(-3, 3),
  plot_labels = TRUE,
  node_label_width = 50,
  group_label_font_size = 1
)

Arguments

  • cell_state_graph
    object
    Contains the cell state graph and layout information.

  • deg_table
    data.frame
    Data frame with DEGs including log fold changes and p-values.

  • perturb_table
    data.frame (optional)
    Perturbation information. Default is NULL.

  • facet_group
    string
    Facet group for plotting. Default is "term".

  • arrow_unit
    numeric
    Arrow size. Default is 7.

  • node_size
    numeric
    Node size. Default is 1.

  • con_colour
    string
    Connection color. Default is "darkgrey".

  • fract_expr
    numeric
    Minimum fraction of expression. Default is 0.0.

  • mean_expr
    numeric
    Minimum mean expression. Default is 0.0.

  • legend_position
    string
    Legend position. Default is "none".

  • fc_limits
    numeric vector
    Limits for fold change scale. Default is c(-3, 3).

  • plot_labels
    logical
    Whether to display labels. Default is TRUE.

  • node_label_width
    numeric
    Width of node labels. Default is 50.

  • group_label_font_size
    numeric
    Font size for group labels. Default is 1.

Value

A ggplot object representing the cell state graph with DEGs plotted.

Examples

# Example usage:
plot_degs(cell_state_graph, deg_table, perturb_table = NULL)