SCpubr (version 3.0.1)

do_TermEnrichmentPlot: Display the enriched terms for a given list of genes.

Description

Display the enriched terms for a given list of genes.

Usage

do_TermEnrichmentPlot(
  mat,
  n.chars = 40,
  n.terms = 25,
  font.size = 14,
  font.type = "sans",
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  use_viridis = FALSE,
  viridis.palette = "G",
  viridis.direction = -1,
  sequential.palette = "YlGnBu",
  sequential.direction = 1,
  dot.scale = 8,
  legend.type = "colorbar",
  legend.position = "bottom",
  legend.framewidth = 0.5,
  legend.tickwidth = 0.5,
  legend.length = 20,
  legend.width = 1,
  legend.framecolor = "grey50",
  legend.tickcolor = "white",
  number.breaks = 5,
  xlab = NULL,
  ylab = NULL,
  na.value = "grey75",
  grid.color = "grey90",
  grid.type = "dashed",
  plot.title.face = "bold",
  plot.subtitle.face = "plain",
  plot.caption.face = "italic",
  axis.title.face = "bold",
  axis.text.face = "plain",
  axis.text.x.angle = 45,
  legend.title.face = "bold",
  legend.text.face = "plain"
)

Value

A dotplot object with enriched terms.

Arguments

mat

list | Result of over-representation test with clusterProfiler. Accepts only one result, be aware of that if you compute the test for all GO ontologies. Accessed through mat@result.

n.chars

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 40.

n.terms

numeric | Number of terms to display. Defaults to 25.

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.

use_viridis

logical | Whether to use viridis color scales.

viridis.palette

character | A capital letter from A to H or the scale name as in scale_fill_viridis.

viridis.direction

numeric | Either 1 or -1. Controls how the gradient of viridis scale is formed.

sequential.palette

character | Type of sequential color palette to use. Out of the sequential palettes defined in brewer.pal.

sequential.direction

numeric | Direction of the sequential color scale. Either 1 or -1.

dot.scale

numeric | Scale the size of the dots.

legend.type

character | Type of legend to display. One of:

• normal: Default legend displayed by ggplot2.

• colorbar: Redefined colorbar legend, using guide_colorbar.

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.framewidth, legend.tickwidth

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

legend.length, legend.width

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

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.

number.breaks

numeric | Controls the number of breaks in continuous color scales of ggplot2-based plots.

xlab, ylab

character | Titles for the X and Y axis.

na.value

character | Color value for NA.

grid.color

character | Color of the grid in the plot. In heatmaps, color of the border of the cells.

grid.type

character | One of the possible linetype options:

• blank.

• solid.

• dashed.

• dotted.

• dotdash.

• longdash.

• twodash.

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.

axis.text.x.angle

numeric | Degree to rotate the X labels. One of: 0, 45, 90.

Examples

# \donttest{
  # 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"))
    
    # Default plot.
    p <- SCpubr::do_TermEnrichmentPlot(mat = enriched_terms)
    
  } 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()`.")
  }
# }