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. DefaultNULL
.- combinePlot
Logical, whether to utilize
plot_grid
to combine multiple plots into one. DefaultTRUE
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
. DefaultTRUE
.- dotColor, dotSize, dotAlpha
Numeric, controls the appearance of all dots. Default
"grey"
,0.6
and0.3
, 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
.- ...
More theme setting arguments passed to
.ggplotLigerTheme
.
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
.