Shared parameter documentation

Arguments

BPPARAM

bpparamClass. BiocParallel parameter to specify the desired processor configuration.
We recommend using one of the following:

FUN

function.

MARGIN

integer(1-2). Dimension where the function will be applied. For a two-dimensional matrix: 1 indicates rows; 2 indicates columns; c(1, 2) indicates rows and columns.

alphaThreshold

numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.

asis

logical(1). Set this to TRUE when using the function inside a loop or inside an R Markdown chunk with 'results = "asis"' enabled.

aspectRatio

integer(1). Aspect ratio.

assay

vector(1). Assay name or index position.

assays

SimpleList. Count matrices, which must have matching dimensions. Counts can be passed in as either a dense matrix (matrix) or sparse matrix (sparseMatrix).

base

integer(1). Logarithm base.

baseMeanThreshold

numeric(1) or NULL. Base mean (i.e. average expression across all samples) threshold. If left NULL, will use the cutoff defined in the object. Applies in general to DESeq2 RNA-seq differential expression output.

borderColor

character(1) or NULL. Border color.

captions

character or NULL. Captions. If NULL, the names of the primary input list will be used automatically.

cells

character. Cell identifiers.

censorSamples

character. Specify a subset of samples to censor.

class

character(1). Object class.

classes

character. Object classes.

closed

logical(2). Should the lower (1) and upper (2) bounaries be closed?

colData

DataFrame. Metadata describing the assay columns. For bulk RNA-seq, this data describes the samples. For single-cell RNA-seq, this data describes the cells.

colnames

logical(1). Apply to column names.

color

ScaleDiscrete. Desired ggplot2 color scale. Must supply discrete values. When set NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().

To set the discrete color palette globally, use:

options("acid.color.discrete" = ggplot2::scale_color_viridis_d())

compress

logical(1) or character(1). These character strings are currently allowed for save(): "gzip", "bzip2", or "xz".

convertGenesToSymbols

logical(1). Attempt to automatically convert gene identifiers to gene symbols. Only applies when object contains mappings defined in rowRanges.

counts

matrix. Count matrix. Normalized counts are recommended.

countsAxisLabel

character(1). Counts axis label.

dark

logical(1). Plot against a dark background using the acid_theme_light() ggplot2 theme.

dims

integer. Vector of length 2 that denotes the columns from the reduced dimension matrix to use for centerX and centerY column calculations. Defaults the first and second dimensions.

dir

character(1). Directory path.

direction

character(1). Include "both", "up", or "down" directions.

ensemblRelease

integer(1). Ensembl release version (e.g. 100). We recommend setting this value if possible, for improved reproducibility. When left unset, the latest release available via AnnotationHub/ensembldb is used. Note that the latest version available can vary, depending on the versions of AnnotationHub and ensembldb in use.

envir

environment. Environment.

expression

character(1). Calculation to apply. Uses match.arg() internally and defaults to the first argument in the character vector.

file

character(1). File path.

fill

ggproto/ScaleDiscrete. Desired ggplot2 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().

To set the discrete fill palette globally, use:

options("acid.fill.discrete" = ggplot2::scale_fill_viridis_d())

flip

logical(1). Flip x and y axes. Recommended for plots containing many samples.

fun

function.

geneToSymbol

GeneToSymbol. Gene-to-symbol mappings. Must contain geneId and geneName columns. See GeneToSymbol for more information.

genes

character. Gene identifiers.

genomeBuild

character(1). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").

gffFile

character(1). GFF/GTF (General Feature Format) file. Generally, we recommend using GTF (GFFv2) instead of GFFv3.

geom

character(1). Plot type. Uses match.arg() internally and defaults to the first argument in the character vector.

headerLevel

integer(1) (1-7). Markdown header level.

i

Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL.

For more information:

help(topic = "Extract", package = "base")

ignoreTxVersion

logical(1). Don't the include the transcript version in the identifier.

inherits

logical(1). Should the enclosing frames of the environment be searched?

interestingGroups

character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.

j

Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL.

For more information:

help(topic = "Extract", package = "base")

label

logical(1). Superimpose sample text labels on the plot.

labelSize

integer(1). Size of the text label.

labels

list. ggplot2 labels. See ggplot2::labs() for details.

lfcThreshold

numeric(1) or NULL. Log (base 2) fold change ratio cutoff threshold. If left NULL, will use the cutoff defined in the object.

level

character(1). Return as genes or transcripts.

legend

logical(1). Include plot legend.

limit

numeric(1). Threshold limit.

lower

numeric(1). Lower boundary.

max

numeric(1). Recommended maximum value cutoff.

metadata

list. Metadata.

metric

character(1). Metric type, either length or elements.

min

numeric(1). Recommended minimum value cutoff.

minCounts

integer(1). Minimum number of counts per feature (i.e. gene).

msg

NULL or character(1). Custom message to return.

nMax

integer(1). or Inf. Maximum number (i.e. of lines) to include. Use Inf to not apply a limit.

n

integer(1). Number to include.

ntop

integer(1). Number of top features to label.

nullOk

logical(1). If set to TRUE, x may also be NULL.

object

Object.

ordered

logical(1).

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

overwrite

logical(1). Overwrite existing file on disk.

pattern

character(1). Pattern to use for matching.

perMillion

logical(1). Display as counts per million.

perSample

logical(1). Visualize the distributions per sample.

pointAlpha

numeric(1) (0-1). Alpha transparency level.

pointColor

character(1). Default point color for the plot.

pointScalar

integer(1). Default point size for the plot.

pointSize

numeric(1). Point size for dots in the plot. In the range of 1-3 is generally recommended.

pointsAsNumbers

logical(1). Plot the points as numbers (TRUE) or dots (FALSE).

prefilter

logical(1). Apply prefiltering. Remove zero count genes.

progress

logical(1). Show progress, using progress bars.

projectDir

character(1). Project directory path.

quiet

logical(1). Perform command quietly, suppressing messages.

reducedDims

SimpleList. List containing matrices of cell coordinates in reduced space.

reduction

vector(1). Dimension reduction name or index position.

release

removeNa

logical(1). Remove NA values from calculations.

return

character(1). Return type. Uses match.arg() internally and defaults to the first argument in the character vector.

rowData

DataFrame. Metadata describing the assay rows, if genomic ranges are not available. Use rowRanges (GenomicRanges) instead, if possible.

rowRanges

GenomicRanges or GenomicRangesList. Genomic ranges (e.g. genome annotations). Metadata describing the assay rows.

rownames

logical(1). Apply to row names.

sampleMetadataFile

character(1). Sample metadata file path. CSV or TSV is preferred, but Excel worksheets are also supported. Check the documentation for conventions and required columns.

samples

character. Sample identifiers.

sigPointColor

character. Color names for labeling upregulated and downregulated genes. Also supports a character string for labeling DEGs with the same color, regardless of direction.

sort

logical(1). Resort using sort.

spikeNames

character. Vector indicating which assay rows denote spike-in sequences (e.g. ERCCs).

subtitle

character(1). Subtitle.

tabset

logical(1). Include tabset marker.

text

character(1). Text.

title

character(1). Title.

traceback

logical(1). Include traceback in error message. See traceback() for details. rlang::entrace() also works nicely and can be set in .Rprofile.

trans

character(1). Name of the axis scale transformation to apply.

For more information:

help(topic = "scale_x_continuous", package = "ggplot2")

transgeneNames

character. Vector indicating which assay rows denote transgenes (e.g. EGFP, TDTOMATO).

trendline

logical(1). Include trendline on plot.

txToGene

TxToGene. Transcript-to-gene mappings.

unicode

logical(1). Allow Unicode characters in console output.

uploadDir

character(1). Final upload directory path.

upper

numeric(1). Upper boundary.

url

character(1). Uniform Resource Locator (URL).

value

Value to assign.

verbose

logical(1). Run the function with verbose output.

x

Object.

y

Object.

yaml

list. YAML metadata.

zeroPropagate

logical(1). Allow propagation of zeroes.

.xname

Name of object defined in x. Not intended to be used directly.

.yname

Name of object defined in y. Not intended to be used directly.

...

Additional arguments.

Value

No value.