plotCellViolin: Generate violin/box plot(s) using liger object

Description

This function allows for using available cell metadata, feature expression or factor loading to generate violin plot, and grouping the data with available categorical cell metadata. Available categorical cell metadata can be used to form the color annotation. When it is different from the grouping, it forms a nested grouping. Multiple y-axis variables are allowed from the same specification of slot, and this returns a list of violin plot for each. Users can further split the plot(s) by grouping on cells (e.g. datasets).

Usage

plotCellViolin(
  object,
  y,
  groupBy = NULL,
  slot = c("cellMeta", "rawData", "normData", "scaleData", "H.norm", "H"),
  yFunc = NULL,
  cellIdx = NULL,
  colorBy = NULL,
  splitBy = NULL,
  titles = NULL,
  ...
)

Value

A ggplot object when a single plot is intended. A list of ggplot objects, when multiple y variables and/or splitBy are set. When plotly = TRUE, all ggplot objects become plotly (htmlwidget) objects.

Arguments

object

liger object

y

Available variable name in slot to look for the value to visualize.

groupBy, colorBy

Available variable name in cellMeta slot to look for categorical grouping. See details. Default NULL produces no grouping and all-black graphic elements.

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.

splitBy

Character vector of categorical variable names in cellMeta slot. Split all cells by groupings on this/these variable(s) to produce a violin plot containing only the cells in each group. Default NULL.

titles

Title text. A character scalar or a character vector with as many elements as multiple plots are supposed to be generated. Default NULL.

...

Arguments passed on to .ggCellViolin, .ggplotLigerTheme

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.

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.

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)/15) columns.

plotly

Whether to use plotly to enable web based interactive browsing for the plot. Requires installation of package "plotly". Default FALSE.

Details

Available option for slot include: "cellMeta", "rawData", "normData", "scaleData", "H.norm" and "H". When "rawData", "normData" or "scaleData", y has to be a character vector of feature names. When "H.norm" or "H", colorBy can be any valid index to select one factor of interests. Note that character index follows "Factor_[k]" format, with replacing [k] with an integer.

When "cellMeta", y has to be an available column name in the table. Note that, for y as well as groupBy, colorBy and splitBy since a matrix object is feasible in cellMeta table, using a column (e.g. named as "column1" in a certain matrix (e.g. named as "matrixVar") should follow the syntax of "matrixVar.column1". When the matrix does not have a "colname" attribute, the subscription goes with "matrixVar.V1", "matrixVar.V2" and etc. These are based on the nature of as.data.frame method on a DataFrame object.

groupBy is basically send to ggplot2::aes(x), while colorBy is for the "colour" aesthetics. Specifying colorBy without groupBy visually creates grouping but there will not be varying values on the x-axis, so boxWidth will be forced to the same value as violinWidth under this situation.

Examples

Run this code

plotCellViolin(pbmcPlot, y = "nUMI", groupBy = "dataset", slot = "cellMeta")
plotCellViolin(pbmcPlot, y = "nUMI", groupBy = "leiden_cluster",
               slot = "cellMeta", splitBy = "dataset",
               colorBy = "leiden_cluster",
               box = TRUE, dot = TRUE,
               ylab = "Total counts per cell")
plotCellViolin(pbmcPlot, y = "S100A8", slot = "normData",
               yFunc = function(x) log2(10000*x + 1),
               groupBy = "dataset", colorBy = "leiden_cluster",
               box = TRUE, ylab = "S100A8 Expression")