do_AlluvialPlot: Generate Alluvial plots.

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

Generate Alluvial plots.

Description

This function is based on the ggalluvial package. It allows you to generate alluvial plots from a given Seurat object.

Usage

do_AlluvialPlot(
  sample,
  first_group,
  last_group,
  middle_groups = NULL,
  colors.use = NULL,
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  font.size = 14,
  font.type = "sans",
  xlab = NULL,
  ylab = "Number of cells",
  repel = FALSE,
  fill.by = last_group,
  use_labels = FALSE,
  stratum.color = "black",
  stratum.fill = "white",
  stratum.width = 1/3,
  stratum.fill.conditional = FALSE,
  use_geom_flow = FALSE,
  alluvium.color = "white",
  flow.color = "white",
  flip = FALSE,
  label.color = "black",
  curve_type = "sigmoid",
  use_viridis = FALSE,
  viridis.palette = "G",
  viridis.direction = -1,
  sequential.palette = "YlGnBu",
  sequential.direction = 1,
  plot.grid = FALSE,
  grid.color = "grey75",
  grid.type = "dashed",
  na.value = "white",
  legend.position = "right",
  legend.title = NULL,
  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

sample	Seurat | A Seurat object, generated by CreateSeuratObject.
first_group	character | Categorical metadata variable. First group of nodes of the alluvial plot.
last_group	character | Categorical metadata variable. Last group of nodes of the alluvial plot.
middle_groups	character | Categorical metadata variable. Vector of groups of nodes of the alluvial plot.
colors.use	character | Named list of colors corresponding to the unique values in fill.by (which defaults to last_group).
plot.title, plot.subtitle, plot.caption	character | Title, subtitle or caption to use in the plot.
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.
xlab, ylab	character | Titles for the X and Y axis.
repel	logical | Whether to repel the text labels.
fill.by	character | One of first_group, middle_groups (one of the values, if multiple mid_groups) or last_group. These values will be used to color the alluvium/flow.
use_labels	logical | Whether to use labels instead of text for the stratum.
stratum.color, alluvium.color, flow.color	character | Color for the border of the alluvium (and flow) and stratum.
stratum.fill	character | Color to fill the stratum.
stratum.width	logical | Width of the stratum.
stratum.fill.conditional	logical | Whether to fill the stratum with the same colors as the alluvium/flow.
use_geom_flow	logical | Whether to use geom_flow instead of geom_alluvium. Visual results might differ.
flip	logical | Whether to invert the axis of the displayed plot.
label.color	character | Color for the text labels.
curve_type	character | Type of curve used in geom_alluvium. One of: linear. cubic. quintic. sine. arctangent. sigmoid. xspline.
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.
plot.grid	logical | Whether to plot grid lines.
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.
na.value	character | Color value for NA.
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.title	character | Title for 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.

Examples

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

    # Compute basic sankey plot.
    p <- SCpubr::do_AlluvialPlot(sample = sample,
                                 first_group = "orig.ident",
                                 last_group = "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()`.")
  }

SCpubr documentation built on Oct. 11, 2023, 5:15 p.m.