plotDensityDimRed: Create density plot basing on specified coordinates

In rliger: Linked Inference of Genomic Experimental Relationships

Create density plot basing on specified coordinates

Description

This function shows the cell density presented in a 2D dimensionality reduction coordinates. Density is shown with coloring and contour lines. A scatter plot of the dimensionality reduction is added as well. The density plot can be splitted by categorical variables (e.g. "dataset"), while the scatter plot will always be shown for all cells in subplots as a reference of the global structure.

Usage

plotDensityDimRed(
  object,
  useDimRed = NULL,
  splitBy = NULL,
  combinePlot = TRUE,
  minDensity = 8,
  contour = TRUE,
  contourLineWidth = 0.3,
  contourBins = 5,
  dot = TRUE,
  dotColor = "grey",
  dotSize = 0.6,
  dotAlpha = 0.3,
  dotRaster = NULL,
  title = NULL,
  legendFillTitle = "Density",
  colorPalette = "magma",
  colorDirection = -1,
  ...
)

Arguments

object	A liger object
useDimRed	Name of the variable storing dimensionality reduction result in the cellMeta slot. Default uses default dimension reduction.
splitBy	Character vector of categorical variable names in cellMeta slot. Split all cells by groupings on this/these variable(s) to produce a density plot containing only the cells in each group. Default NULL.
combinePlot	Logical, whether to utilize plot_grid to combine multiple plots into one. Default TRUE returns combined ggplot. FALSE returns a list of ggplot or a single ggplot when only one plot is requested.
minDensity	A positive number to filter out low density region colored on plot. Default 8. Setting zero will show density on the whole panel.
contour	Logical, whether to draw the contour line. Default TRUE.
contourLineWidth	Numeric, the width of the contour line. Default 0.3.
contourBins	Number of contour bins. Higher value generates more contour lines. Default 5.
dot	Logical, whether to add scatter plot of all cells, even when density plot is splitted with splitBy. Default TRUE.
dotColor, dotSize, dotAlpha	Numeric, controls the appearance of all dots. Default "grey", 0.6 and 0.3, respectively.
dotRaster	Logical, whether to rasterize the scatter plot. Default NULL automatically rasterizes the dots when number of total cells to be plotted exceeds 100,000.
title	Text of main title of the plots. Default NULL. Length of character vector input should match with number of plots generated.
legendFillTitle	Text of legend title. Default "Density".
colorPalette	Name of the option for scale_fill_viridis_c. Default "magma".
colorDirection	Color gradient direction for scale_fill_viridis_c. Default -1.
...	Arguments passed on to .ggplotLigerTheme title,subtitle,xlab,ylab Main title, subtitle or X/Y axis title text. By default, no main title or subtitle will be set, and X/Y axis title will be the names of variables used for plotting. Use NULL to hide elements. TRUE for xlab or ylab shows default values. showLegend Whether to show the legend. Default TRUE. legendPosition Text indicating where to place the legend. Choose from "top", "bottom", "left" or "right". Default "right". baseSize One-parameter control of all text sizes. Individual text element sizes can be controlled by other size arguments. "Title" sizes are 2 points larger than "text" sizes when being controlled by this. titleSize,xTitleSize,yTitleSize,legendTitleSize Size of main title, axis titles and legend title. Default NULL controls by baseSize + 2. subtitleSize,xTextSize,yTextSize,legendTextSize Size of subtitle text, axis texts and legend text. Default NULL controls by baseSize. panelBorder Whether to show rectangle border of the panel instead of using ggplot classic bottom and left axis lines. Default FALSE. plotly Whether to use plotly to enable web based interactive browsing for the plot. Requires installation of package "plotly". Default FALSE.

Value

A ggplot object when only one plot is generated, A ggplot object combined with plot_grid when multiple plots and combinePlot = TRUE. A list of ggplot when multiple plots and combinePlot = FALSE.

Examples

# Example dataset has small number of cells, thus cutoff adjusted.
plotDensityDimRed(pbmcPlot, minDensity = 1)

rliger documentation built on Oct. 30, 2024, 1:07 a.m.