general: General Arguments

Description Arguments Value

Description

General Arguments

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.

Value

No value.


WeiSong-bio/roryk-bcbioSinglecell documentation built on July 6, 2019, 12:03 a.m.