params: Shared parameter documentation
In acidgenomics/r-acidroxygen: Acid Genomics Documentation

params

R Documentation

Shared parameter documentation

Description

Shared parameter documentation

Arguments

`BPPARAM`	`bpparamClass`. BiocParallel parameter to specify the desired processor configuration. We recommend using one of the following: bpparam. SerialParam. MulticoreParam.
`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`	`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.
`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.