Plot EnhancedVolcano

Plot EnhancedVolcano

plot_EnhancedVolcano(
  genelist,
  effectsize_threshold = 1,
  pvalue_threshold = 0.05,
  background_color = "black",
  foreground_color = "white",
  interactive = FALSE,
  legend_labels = c("NS", "FC", "P", "FC & P"),
  x_label = "effectsize (FC)",
  y_label = "-log10(pvalue) (P)",
  title = "Volcano plot",
  subtitle = "EnhancedVolcano",
  caption = paste0("N genes: ", nrow(genelist)),
  label_size = 3,
  legend_label_size = 14,
  axes_label_size = 18,
  point_size = 2
)

Arguments

genelist

UI value/list of tibbles/dataframes

effectsize_threshold

numeric, default: 1, threshold for showing significance on effectsize axis

pvalue_threshold

numeric, default: 0.05, threshold for showing significance on pvalue axis

background_color

default: 'black', else character hexcolor or colorname

foreground_color

default: 'white', else character hexcolor or colorname

interactive

default: FALSE, else TRUE

legend_labels

character vector, default: c('NS', 'FC', 'P', 'FC & P'), plot legend labels

x_label

character, default: 'effectsize (FC)', plot x-axis label

y_label

character, default: "'-log10(pvalue) (P)', plot y-axis label

title

character, default: 'Volcano plot', plot title

subtitle

character, default: 'EnhancedVolcano', plot subtitle

caption

character, default: paste0("N genes: ", nrow(genelist)), plot caption

label_size

numeric, default: 3, plot variable label size

legend_label_size

numeric, default: 14, plot legend label size

axes_label_size

numeric, default: 18, plot x- and y-axis lable sizes

point_size

numeric, default: 2, plot point size

Value

plotly or ggplot2 object

Examples

plot_EnhancedVolcano(
  get(load(system.file("extdata", "example_genelist.rda", package = "goatea")))
)
#> 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.
#> Coordinate system already present.
#> ℹ Adding new coordinate system, which will replace the existing one.
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Warning: ggrepel: 11 unlabeled data points (too many overlaps). Consider increasing max.overlaps