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Generate violin/box plot(s) using liger object

Source: R/ggplotting.R
plotCellViolin.Rd

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,
  ...
)

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.

...

More plot setting arguments. See .ggCellViolin and .ggplotLigerTheme.

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.

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

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",
               colorValues = RColorBrewer::brewer.pal(8, "Set1"))
#> $nUMI.ctrl
#> Warning: Duplicated `override.aes` is ignored.

#> 
#> $nUMI.stim
#> Warning: Duplicated `override.aes` is ignored.

#> 
plotCellViolin(pbmcPlot, y = "S100A8", slot = "normData",
               yFunc = function(x) log2(10000*x + 1),
               groupBy = "dataset", colorBy = "leiden_cluster",
               box = TRUE, ylab = "S100A8 Expression")
#> Warning: Duplicated `override.aes` is ignored.