Package 'scLang'

Title: A unified language for interacting with Seurat and SingleCellExperiment
Description: scLang is a suite for package development for scRNA-seq analysis. It offers functions that can operate on both Seurat and SingleCellExperiment objects. These functions are primarily aimed to help developers build tools compatible with both types of input.
Authors: Andrei-Florian Stoica [aut, cre] (ORCID: <https://orcid.org/0000-0002-5253-0826>)
Maintainer: Andrei-Florian Stoica <[email protected]>
License: MIT + file LICENSE
Version: 1.1.3
Built: 2026-05-07 11:15:55 UTC
Source: https://github.com/bioc/scLang

Help Index

Creates a dimensionality reduction plot

Description

This function creates a dimensionality reduction plot

Usage

dimPlot(
  scObj,
  groupBy = NULL,
  title = NULL,
  dimred = "umap",
  dims = c(1, 2),
  legendTitle = "Group",
  noGroupsLegendLab = "Object",
  palette = "grDevices::rainbow",
  pointSize = 0.5,
  alpha = 0.7,
  legendPos = c("right", "top", "left", "bottom"),
  legendTextSize = 10,
  legendTitleSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  ...
)

Arguments

scObj

A Seurat or SingleCellExperiment object.
groupBy

Grouping variable. Must exist in the metadata/coldata of the single-cell expression object.
title

Plot title.
dimred

Dimensionality reduction.
dims

A numeric vector of size 2 representing the dimensions selected for the plot.
legendTitle

Legend title.
noGroupsLegendLab

Legend label to be used when no grouping is provided (groupBy is NULL)
palette

Color palette.
pointSize

Point size.
alpha

Opaqueness level.
legendPos

Legend position.
legendTextSize

Legend text size.
legendTitleSize

Legend title size.
axisTextSize

Axis text size.
axisTitleSize

Axis title size.
...

Additional arguments passed to henna::centerTitle.

Value

A dimensionality reduction plot.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
dimPlot(sceObj, groupBy='Donor')

Extract the names of available dimensionality reductions from object

Description

This function extracts the names of available dimensionality reductions from a Seurat or SingleCellExperiment object.

Usage

## Default S3 method:
dimredNames(scObj)

## S3 method for class 'Seurat'
dimredNames(scObj)

## S3 method for class 'SingleCellExperiment'
dimredNames(scObj)

dimredNames(scObj)

Arguments

scObj

A Seurat or SingleCellExperiment object.

Value

A character vector.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
dimredNames(sceObj)

Create a dimensionality reduction plot to represent a feature

Description

This function creates a dimensionality reduction plot to represent a feature (gene expression or numeric metadata column).

Usage

featurePlot(
  scObj,
  feature = rownames(scObj)[1],
  title = feature,
  dimred = "umap",
  dims = c(1, 2),
  legendTitle = NULL,
  palette = paletteer_d("wesanderson::Royal1")[c(3, 2)],
  pointSize = 0.5,
  alpha = 0.6,
  legendPos = c("right", "top", "left", "bottom"),
  legendTextSize = 10,
  legendTitleSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  ...
)

Arguments

scObj

A Seurat or SingleCellExperiment object.
feature

A gene name or metadata column name.
title

Plot title.
dimred

Dimensionality reduction.
dims

A numeric vector of size 2 representing the dimensions selected for the plot.
legendTitle

Legend title.
palette

Color palette.
pointSize

Point size.
alpha

Opaqueness level.
legendPos

Legend position.
legendTextSize

Legend text size.
legendTitleSize

Legend title size.
axisTextSize

Axis text size.
axisTitleSize

Axis title size.
...

Additional arguments passed to henna::centerTitle.

Value

A feature plot.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
featurePlot(sceObj, 'Gene289')

Extract metadata from object as a data frame

Description

This function extracts the metadata from a Seurat or SingleCellExperiment object as a data frame.

Usage

metadataDF(scObj)

## Default S3 method:
metadataDF(scObj)

## S3 method for class 'Seurat'
metadataDF(scObj)

## S3 method for class 'SingleCellExperiment'
metadataDF(scObj)

Arguments

scObj

A Seurat or SingleCellExperiment object.

Value

A metadata data frame.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
df <- metadataDF(sceObj)

Return metadata names

Description

This function extracts metadata names from a Seurat or SingleCellExperiment object. It can also be used to modify metadata names.

Usage

metadataNames(scObj)

Arguments

scObj

A Seurat or SingleCellExperiment object.

Value

The names of the metadata columns.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
colNames <- metadataNames(sceObj)

Extract a metadata/coldata column from object.

Description

This function extracts a metadata/coldata column from a Seurat or SingleCellExperiment object.

Usage

scCol(scObj, col)

scCol(scObj, col) <- value

## Default S3 method:
scCol(scObj, col)

## Default S3 replacement method:
scCol(scObj, col) <- value

## S3 method for class 'Seurat'
scCol(scObj, col)

## S3 replacement method for class 'Seurat'
scCol(scObj, col) <- value

## S3 method for class 'SingleCellExperiment'
scCol(scObj, col)

## S3 replacement method for class 'SingleCellExperiment'
scCol(scObj, col) <- value

Arguments

scObj

A Seurat or SingleCellExperiment object.
col

Column name.
value

A vector to be added to the metadata/coldata of the single-cell expression object.

Value

A vector.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
v <- scCol(sceObj, 'Cluster')

Extract per-group counts from the column of a single-cell expression object

Description

This function extracts per-group counts from the column of single-cell expression object.

Usage

scColCounts(scObj, col)

Arguments

scObj

A Seurat or SingleCellExperiment object.
col

Column as string.

Value

A frequency vector with the unique column values as names.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
scColCounts(sceObj, 'Cluster')

Extract counts from two columns of a single-cell expression object

Description

This function extracts count information from two columns of a single-cell expression object.

Usage

scColPairCounts(scObj, col1, col2)

Arguments

scObj

A Seurat or SingleCellExperiment object.
col1

Column as string.
col2

Column as string.

Value

A data frame listing the counts of all combinations of pairs from two categorical columns.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
scColPairCounts(sceObj, 'Cluster', 'Donor')

Extract percentages from two columns of a single-cell expression object

Description

This function extracts percentage information from two columns of a single-cell expression object. For each i x j combination with i taken from column 1 and j taken from column 2, the function reports the percentage that j contributes to all combinations involving i.

Usage

scColPairPercs(scObj, col1, col2, sigDigits = 2)

Arguments

scObj

A Seurat or SingleCellExperiment object.
col1

Column as string.
col2

Column as string.
sigDigits

Number of significant digits.

Value

A data frame listing the percentages of all combinations of pairs from two categorical columns.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
scColPairPercs(sceObj, 'Cluster', 'Donor')

Extract observed-over-expected ratios from two columns of a single-cell expression object

Description

This function extracts observed-over-expected ratios from two columns of a single-cell expression object.

Usage

scColPairRatios(scObj, col1, col2, sigDigits = 2)

Arguments

scObj

A Seurat or SingleCellExperiment object.
col1

Column as string.
col2

Column as string.
sigDigits

Number of significant digits.

Value

A data frame listing the observed-over-expected ratios of all combinations of pairs from two categorical columns.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
scColPairRatios(sceObj, 'Cluster', 'Donor')

Extracts a dimensionality reduction matrix from object.

Description

This function extracts a dimensionality reduction matrix from a Seurat or SingleCellExperiment object.

Usage

## Default S3 method:
scDimredMat(scObj, dimred)

## S3 method for class 'Seurat'
scDimredMat(scObj, dimred)

## S3 method for class 'SingleCellExperiment'
scDimredMat(scObj, dimred)

scDimredMat(scObj, dimred)

Arguments

scObj

A Seurat or SingleCellExperiment object.
dimred

Dimensionality reduction.

Value

A dimensionality reduction matrix.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
pcaMat <- scDimredMat(sceObj, 'pca')

Extracts the expression matrix from object.

Description

This function extracts an expression matrix from a Seurat or SingleCellExperiment object. For additional flexibility, the input can alternatively be provided as a dgCMatrix object (and an option to densify it is also available) or as a matrix object.

Usage

## Default S3 method:
scExpMat(scObj, slot = NULL, genes = NULL, densify = TRUE)

## S3 method for class 'Seurat'
scExpMat(scObj, slot = "data", genes = NULL, densify = TRUE)

## S3 method for class 'SingleCellExperiment'
scExpMat(scObj, slot = "logcounts", genes = NULL, densify = TRUE)

## S3 method for class 'dgCMatrix'
scExpMat(scObj, slot = NULL, genes = NULL, densify = TRUE)

## S3 method for class 'matrix'
scExpMat(scObj, slot = NULL, genes = NULL, densify = TRUE)

scExpMat(scObj, slot, genes = NULL, densify = TRUE)

Arguments

scObj

A Seurat, SingleCellExperiment, dgCMatrix or matrix object.
slot

Gene expression slot. Ignored if scObj is of class dgCMatrix or matrix.
genes

Selected genes. If NULL, all genes will be retained.
densify

Whether to convert to dense matrix.

Value

An expression matrix.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
mat <- scExpMat(sceObj, 'counts')

Extracts the expression of a single gene

Description

This function extracts the expression of a single gene from a Seurat, SingleCellExperiment, dgCMatrix or matrix object.

Usage

## Default S3 method:
scGeneExp(scObj, gene, slot = NULL)

## S3 method for class 'Seurat'
scGeneExp(scObj, gene, slot = "data")

## S3 method for class 'SingleCellExperiment'
scGeneExp(scObj, gene, slot = "logcounts")

## S3 method for class 'dgCMatrix'
scGeneExp(scObj, gene, slot = NULL)

## S3 method for class 'matrix'
scGeneExp(scObj, gene, slot = NULL)

scGeneExp(scObj, gene, slot)

Arguments

scObj

A Seurat, SingleCellExperiment, dgCMatrix or matrix object.
gene

Selected gene.
slot

Gene expression slot. Ignored if scObj is of class dgCMatrix or matrix.

Value

A gene expression vector.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
v <- scGeneExp(sceObj, 'Gene291')

Extracts the PCA matrix from object.

Description

This function extracts the PCA matrix from a Seurat or SingleCellExperiment object.

Usage

scPCAMat(scObj)

Arguments

scObj

A Seurat or SingleCellExperiment object.

Value

A PCA matrix.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
pcaMat <- scPCAMat(sceObj)

Extracts the UMAP matrix from object.

Description

This function extracts the UMAP matrix from a Seurat or SingleCellExperiment object.

Usage

scUMAPMat(scObj)

Arguments

scObj

A Seurat or SingleCellExperiment object.

Value

A UMAP matrix.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
umapMat <- scUMAPMat(sceObj)

Create a violin plot to represent a feature

Description

This function creates a violin plot to represent a feature (gene expression or numeric metadata column).

Usage

violinPlot(
  scObj,
  feature = rownames(scObj)[1],
  groupBy = metadataNames(scObj)[1],
  title = feature,
  legendTitle = NULL,
  xLab = "Identity",
  yLab = "Expression level",
  palette = "grDevices::rainbow",
  pointSize = 0.5,
  alpha = 0.8,
  legendPos = c("right", "top", "left", "bottom"),
  legendTextSize = 10,
  legendTitleSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  xLabAngle = 45,
  xLabVjust = 0.5,
  ...
)

Arguments

scObj

A Seurat or SingleCellExperiment object.
feature

A gene name or metadata column name.
groupBy

Grouping variable. Must exist in the metadata/coldata of the single-cell expression object.
title

Plot title.
legendTitle

Legend title.
xLab

x axis label.
yLab

y axis label.
palette

Color palette.
pointSize

Point size.
alpha

Opaqueness level.
legendPos

Legend position.
legendTextSize

Legend text size.
legendTitleSize

Legend title size.
axisTextSize

Axis text size.
axisTitleSize

Axis title size.
xLabAngle

x axis label angle.
xLabVjust

x axis label vertical justification in [0, 1].
...

Additional arguments passed to henna::centerTitle.

Value

A violin plot.

Examples

scePath <- system.file('extdata', 'sceObj.qs2', package='scLang')
sceObj <- qs2::qs_read(scePath)
violinPlot(sceObj, 'Gene289')