Visualize gene expression or cell metadata with violin plot

Usage

plotGeneViolin(object, gene, byDataset = TRUE, groupBy = NULL, ...)

plotTotalCountViolin(object, groupBy = "dataset", ...)

plotGeneDetectedViolin(object, groupBy = "dataset", ...)

Arguments

object

A liger object.

gene

Character gene names.

byDataset

Logical, whether the violin plot should be splitted by dataset. Default TRUE.

groupBy

Names of available categorical variable in cellMeta slot. Use FALSE for no grouping. Default NULL looks clustering result but will not group if no clustering found.

...

Arguments passed on to plotCellViolin, .ggCellViolin, .ggplotLigerTheme

slot: Choose the slot to find the y variable. See Details. Default "cellMeta".
yFunc: A function object that expects a vector/factor/data.frame retrieved by y as the only input, and returns an object of the same size, so that the y-axis is replaced by this output. Useful when, for example, users need to scale the gene expression shown on plot.
cellIdx: Character, logical or numeric index that can subscribe cells. Missing or NULL for all cells.
titles: Title text. A character scalar or a character vector with as many elements as multiple plots are supposed to be generated. Default NULL.
violin,box,dot: Logical, whether to add violin plot, box plot or dot (scatter) plot, respectively. Layers are added in the order of dot, violin, and violin on the top surface. By default, only violin plot is generated.
violinAlpha,boxAlpha: Numeric, controls the transparency of layers. Default 0.8, 0.6, respectively.
violinWidth,boxWidth: Numeric, controls the width of violin/box bounding box. Default 0.9 and 0.4.
dotColor,dotSize: Numeric, globally controls the appearance of all dots. Default "black" and getOption("ligerDotSize") (1).
xlabAngle: Numeric, counter-clockwise rotation angle of X axis label text. Default 45.
raster: Logical, whether to rasterize the dot plot. Default NULL automatically rasterizes the dot plot when number of total cells to be plotted exceeds 100,000.
seed: Random seed for reproducibility. Default 1.
legendFillTitle: Legend title text for fill aesthetics, often used for violin, box, bar plots. Default NULL shows the original variable name.
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.
colorLabels: Character vector for modifying category names in a color legend. Passed to ggplot2::scale_color_manual(labels). Default NULL uses original levels of the factor.
colorValues: Character vector of colors for modifying category colors in a color legend. Passed to ggplot2::scale_color_manual(values). Default NULL uses internal selected palette when <= 26 categories are presented, otherwise ggplot hues.
legendNRow,legendNCol: Integer, when too many categories in one variable, arranges number of rows or columns. Default NULL, automatically split to ceiling(levels(variable)/10) columns.
plotly: Whether to use plotly to enable web based interactive browsing for the plot. Requires installation of package "plotly". Default FALSE.

Value

ggplot if using a single gene and not splitting by dataset. Otherwise, list of ggplot.

Examples

plotGeneViolin(pbmcPlot, varFeatures(pbmcPlot)[1],
               groupBy = "leiden_cluster")
#> $ISG15.ctrl

#> 
#> $ISG15.stim

#> 
plotTotalCountViolin(pbmc)

plotGeneDetectedViolin(pbmc, dot = TRUE, box = TRUE, colorBy = "dataset")