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

In enblacar/SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

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"
)

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.

Value

A dotplot 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"))
    
    # 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()`.")
  }

enblacar/SCpubr documentation built on Feb. 11, 2024, 4:15 a.m.