do_WafflePlot: 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_WafflePlot(
  sample,
  group.by,
  waffle.size = 2,
  flip = TRUE,
  colors.use = NULL,
  na.value = "grey75",
  font.size = 14,
  font.type = "sans",
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  legend.title = NULL,
  legend.ncol = NULL,
  legend.nrow = NULL,
  legend.byrow = FALSE,
  legend.position = "bottom",
  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",
  strip.text.face = "bold"
)

Arguments

sample	Seurat | A Seurat object, generated by CreateSeuratObject.
group.by	character | Metadata variable to group the output by. Has to be a character of factor column.
waffle.size	numeric | Tile border size.
flip	logical | Whether to invert the axis of the displayed plot.
colors.use	named_vector | Named vector of valid color representations (either name of HEX codes) with as many named colors as unique values of group.by. If group.by is not provided, defaults to the unique values of Idents. If not provided, a color scale will be set by default.
na.value	character | Color value for NA.
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.title	character | Title for the legend.
legend.ncol	numeric | Number of columns in the legend.
legend.nrow	numeric | Number of rows in the legend.
legend.byrow	logical | Whether the legend is filled by row or not.
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.
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.
strip.text.face	character | Controls the style of the font for the strip text. 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 a Waffle Plot.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_WafflePlot", passive = TRUE)
  
  if (isTRUE(value)){
    # Consult the full documentation in https://enblacar.github.io/SCpubr-book/
    
    # Define your Seurat object.
    sample <- readRDS(system.file("extdata/seurat_dataset_example.rds", package = "SCpubr"))
    
    # Basic Waffle plot.
    p <- SCpubr::do_WafflePlot(sample = sample,
                               group.by = "seurat_clusters")
    
    
  } 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.