Generate a volcano plot for a comparison in a VISTA object

Wraps EnhancedVolcano to visualize log2FC vs p-values for a selected comparison.

Usage

get_volcano_plot(
  x,
  sample_comparison,
  log2fc_cutoff = NULL,
  pval_cutoff = NULL,
  p_value_type = NULL,
  label_genes = NULL,
  label_size = 3,
  point_size = 1,
  colors = c(Up = "#a40000", Down = "#007e2f", Other = "grey"),
  repair_genes = TRUE,
  display_id = NULL,
  display_from = NULL,
  display_orgdb = NULL,
  ...
)

Arguments

x: A VISTA object containing differential expression results.
sample_comparison: Character scalar naming the comparison to display.
log2fc_cutoff: Numeric absolute log2 fold-change threshold used to color significant points. Defaults to cutoffs(x)$log2fc.
pval_cutoff: Numeric p-value threshold used to color significant points. Defaults to cutoffs(x)$pval.
p_value_type: Which p-value column to place on the y-axis and threshold against: "padj" or "pvalue". Defaults to cutoffs(x)$p_value_type.
label_genes: Optional character vector of gene identifiers to force-label.
label_size: Numeric label text size.
point_size: Numeric point size.
colors: Named colour vector with entries for "Up", "Down", and "Other".
repair_genes: Logical; when TRUE, split gene_id values like ID:SYMBOL to display the symbol.
display_id: Optional ID/column name to use for plot labels. If supplied and present in rowData(x), those values are used; otherwise falls back to ID mapping.
display_from: Optional source ID type for mapping (used when display_id is not found in rowData).
display_orgdb: Optional OrgDb object used for ID mapping when display_id is set but not found in rowData.
...: Additional parameters forwarded to EnhancedVolcano::EnhancedVolcano().

Value

A ggplot2 object.

Details

By default the plot inherits the thresholds the object was built with, so the genes coloured here match the ones reported by deg_summary(), get_deg_count_barplot(), and get_genes_by_regulation(). Specifically, log2fc_cutoff, pval_cutoff, and p_value_type default to cutoffs(x)$log2fc, cutoffs(x)$pval, and cutoffs(x)$p_value_type. Supplying any of them explicitly overrides the stored value for that argument only.

Objects created before VISTA 1.1.1, and objects whose stored p_value_type column is absent from the DE table, fall back to the raw pvalue column.

Examples

vista <- example_vista()
comps <- names(comparisons(vista))
get_volcano_plot(vista, sample_comparison = comps[1])
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the EnhancedVolcano package.
#>   Please report the issue to the authors.
#> Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
#> ℹ Please use the `linewidth` argument instead.
#> ℹ The deprecated feature was likely used in the EnhancedVolcano package.
#>   Please report the issue to the authors.


# \donttest{
# Create VISTA object
data("count_data", package = "VISTA")
data("sample_metadata", package = "VISTA")

vista <- create_vista(
  counts = count_data,
  sample_info = sample_metadata,
  column_geneid = "gene_id",
  group_column = "cond_long",
  group_numerator = "treatment1",
  group_denominator = "control"
)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing

# Basic volcano plot
comps <- names(comparisons(vista))
get_volcano_plot(vista, sample_comparison = comps[1])


# With custom thresholds (overrides the stored cutoffs)
get_volcano_plot(
  vista,
  sample_comparison = comps[1],
  log2fc_cutoff = 1.5,
  pval_cutoff = 0.01
)


# Force the raw p-value axis regardless of how the object was built
get_volcano_plot(
  vista,
  sample_comparison = comps[1],
  p_value_type = "pvalue"
)


# Highlight specific genes
genes_of_interest <- rownames(vista)[seq_len(5)]
get_volcano_plot(
  vista,
  sample_comparison = comps[1],
  label_genes = genes_of_interest
)

# }