plot_gene_expr

Plots gene expression data on a cell state graph.

plot_gene_expr(
  cell_state_graph,
  genes,
  arrow_unit = 7,
  con_colour = "lightgrey",
  fract_expr = 0.0,
  mean_expr = 0.0,
  legend_position = "right",
  plot_labels = TRUE,
  aggregate = FALSE,
  scale_to_range = FALSE,
  log_expr = FALSE,
  node_size,
  pseudocount = 1e-5,
  expr_limits = NULL,
  node_label_width = 50,
  group_label_font_size = 1
)

Arguments

• cell_state_graph
  object
  Cell state graph data.

• genes
  vector
  Gene names to plot.

• arrow_unit
  numeric
  Size of arrows in the plot. Default is 7.

• con_colour
  character
  Color for connections. Default is "lightgrey".

• fract_expr
  numeric
  Minimum fraction of cells expressing the gene. Default is 0.0.

• mean_expr
  numeric
  Minimum mean expression level. Default is 0.0.

• legend_position
  character
  Legend position. Default is "right".

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

• aggregate
  logical
  Aggregate gene expression data. Default is FALSE.

• scale_to_range
  logical
  Scale expression data to range. Default is FALSE.

• log_expr
  logical
  Log-transform expression data. Default is FALSE.

• node_size
  numeric
  Offset used to prevent clipping when saving plots.

• pseudocount
  numeric
  Pseudocount for log transformation. Default is 1e-5.

• expr_limits
  numeric vector
  Length 2 vector specifying expression limits. Default is NULL.

• 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 ggplot2 object representing the gene expression on the cell state graph.

Examples

# Example usage:
# plot_gene_expr(cell_state_graph, genes = c("Gene1", "Gene2"))