general: General Arguments
In roryk/bcbioSinglecell: Single-Cell RNA-Seq Utilities

General Arguments

`aspectRatio`	Aspect ratio.
`color`	Desired ggplot color scale. Must supply discrete values. When set to `NULL`, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using `ggplot2::scale_color_manual()`.
`fill`	Desired ggplot fill scale. Must supply discrete values. When set to `NULL`, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using `ggplot2::scale_fill_manual()`.
`gene2symbol`	`data.frame` containing gene-to-symbol mappings. Columns must contain `geneID` and `geneName`.
`dark`	Plot against a dark background using `basejump::theme_midnight()`.
`dir`	Output directory.
`expression`	Calculation to apply. Uses `match.arg()` and defaults to the first argument in the vector.
`genes`	Gene identifiers. Must match the rownames of the object.
`geom`	Plot type. Uses `match.arg()` and defaults to the first argument in the vector.
`grid`	Show major grid lines but hide axis lines.
`headerLevel`	R Markdown header level.
`interestingGroups`	Character vector of interesting groups. Must be formatted in camel case and intersect with `sampleData()` colnames.
`label`	Overlay a cluster identitiy label on the plot.
`labelSize`	Size of the text label.
`legend`	Include plot legend.
`min`	Recommended minimum value cutoff.
`max`	Recommended maximum value cutoff.
`object`	Object.
`pipeline`	Pipeline used to generate the samples.
`pointAlpha`	Alpha transparency level. Useful when there many cells in the dataset, and some cells can be masked.
`pointsAsNumbers`	Plot the points as numbers (`TRUE`) or dots (`FALSE`).
`pointSize`	Cell point size.
`reduction`	Dimensional reduction method to apply. Defaults to t-SNE ("`TSNE`") but UMAP is also supported ("`UMAP`").
`return`	Return type. Uses `base::match.arg()` internally and defaults to the first argument in the vector.
`title`	Plot title.
`trans`	Name of the axis scale transformation to apply. See `help("scale_x_continuous", "ggplot2")` for more information.
`trendline`	Include trendline on plot.
`value`	Object to assign.
`x`	Primary object.
`y`	Secondary object.
`...`	Additional arguments.