do_TermEnrichmentPlot {SCpubr}

Display the enriched terms for a given list of genes.

Description

Display the enriched terms for a given list of genes.

Usage

do_TermEnrichmentPlot(
  enriched_terms,
  nchar_wrap = 20,
  nterms = 10,
  font.size = 14,
  font.type = "sans",
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  legend.position = "bottom",
  legend.type = "colorbar",
  colors.use = NULL,
  text_labels_size = 4,
  legend.length = 30,
  legend.width = 1,
  legend.framewidth = 0.5,
  legend.tickwidth = 0.5,
  legend.framecolor = "grey50",
  legend.tickcolor = "white",
  plot.title.face = "bold",
  plot.subtitle.face = "plain",
  plot.caption.face = "italic",
  axis.title.face = "bold",
  axis.text.face = "plain",
  legend.title.face = "bold",
  legend.text.face = "plain"
)

Arguments

enriched_terms

list | List containing the output(s) of running Enrichr.

nchar_wrap

numeric | Number of characters to use as a limit to wrap the term names. The higher this value, the longer the lines would be for each term in the plots. Defaults to 60.

nterms

numeric | Number of terms to report for each database. Terms are arranged by adjusted p-value and selected from lowest to highest. Defaults to 5.

• Enrichr.

• FlyEnrichr.

• WormEnrichr.

• YeastEnrichr.

• FishEnrichr.

font.size

numeric | Overall font size of the plot. All plot elements will have a size relationship with this font size.

font.type

character | Base font family for the plot. One of:

• mono: Mono spaced font.

• serif: Serif font family.

• sans: Default font family.

plot.title, plot.subtitle, plot.caption

character | Title, subtitle or caption to use in the plot.

legend.position

character | Position of the legend in the plot. One of:

• top: Top of the figure.

• bottom: Bottom of the figure.

• left: Left of the figure.

• right: Right of the figure.

• none: No legend is displayed.

legend.type

character | Type of legend to display. One of:

• normal: Default legend displayed by ggplot2.

• colorbar: Redefined colorbar legend, using guide_colorbar.

colors.use

character | Character vector of 2 colors (low and high ends of the color scale) to generate the gradient.

text_labels_size

numeric | Controls how big or small labels are in the plot.

legend.length, legend.width

numeric | Length and width of the legend. Will adjust automatically depending on legend side.

legend.framewidth, legend.tickwidth

numeric | Width of the lines of the box in the legend.

legend.framecolor

character | Color of the lines of the box in the legend.

legend.tickcolor

character | Color of the ticks of the box in the legend.

plot.title.face, plot.subtitle.face, plot.caption.face, axis.title.face, axis.text.face, legend.title.face, legend.text.face

character | Controls the style of the font for the corresponding theme element. One of:

• plain: For normal text.

• italic: For text in itallic.

• bold: For text in bold.

• bold.italic: For text both in itallic and bold.

Value

A ggplot2 object with enriched terms.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_TermEnrichmentPlot", passive = TRUE)

  if (isTRUE(value)){
    # Consult the full documentation in https://enblacar.github.io/SCpubr-book/

    # Define your enriched terms.
    enriched_terms <- readRDS(system.file("extdata/enriched_terms_example.rds", package = "SCpubr"))
    enriched_terms$GO_Cellular_Component_2021 <- NULL
    enriched_terms$Azimuth_Cell_Types_2021 <- NULL

    # Default plot.
    p <- SCpubr::do_TermEnrichmentPlot(enriched_terms = enriched_terms)
    p
  } else if (base::isFALSE(value)){
    message("This function can not be used without its suggested packages.")
    message("Check out which ones are needed using `SCpubr::state_dependencies()`.")
  }