This function generates either an effect size plot or a volcano plot based on ALDEx2 results.

aldex_volcano_plot(
  table,
  metadata,
  col_cond,
  type = "volcano",
  col_inf = "blue",
  col_sup = "red",
  threshold_lower = -1.5,
  threshold_upper = 1.5,
  cond = NULL,
  cutoff.pval = 0.05,
  show_labels = TRUE,
  taxa = NULL,
  save_table = TRUE,
  table_filename = "aldex_pval_effect.txt"
)

Arguments

table: Data frame with count data; columns represent samples, rows represent features.
metadata: Data frame containing metadata for the samples.
col_cond: Name of the column in metadata that contains the experimental conditions.
type: Type of plot to generate: "effect" for effect size plot or "volcano" for volcano plot.
col_inf: Color for points with effect size/difference lower than threshold (default for "effect" plot).
col_sup: Color for points with effect size/difference higher than threshold (default for "effect" plot).
threshold_lower: Lower threshold for effect size/difference (x-axis).
threshold_upper: Upper threshold for effect size/difference (x-axis).
cond: Name of the condition that appears first in table (used in plot labels).
cutoff.pval: p-value cutoff for significance (default = 0.05).
show_labels: Logical. Whether to display "Higher/Lower in cond" labels (for "effect" plot only, default is TRUE).
taxa: Data frame with taxonomic information (required for "volcano" plot only).

Value

A ggplot object with the selected plot.

Examples

aldex_volcano_plot(table = table,
                    metadata = metadata,
                    col_inf = "blue",
                    col_sup = "red",
                    col_cond = "metodo",
                    type = "effect",
                    threshold_lower = -1,
                    threshold_upper = 1,
                    cond = "kit",
                    show_labels = TRUE)
#> Warning: package 'ggtext' was built under R version 4.4.3
#> Error: object 'metadata' not found