Package 'CytoSimplex'

Title: Simplex Visualization of Cell Fate Similarity in Single-Cell Data
Description: Create simplex plots to visualize the similarity between single-cells and selected clusters in a 1-/2-/3-simplex space. Velocity information can be added as an additional layer. See Liu J, Wang Y et al (2023) <doi:10.1101/2023.12.07.570655> for more details.
Authors: Yichen Wang [aut, cre] , Jialin Liu [aut] , Joshua Welch [cph]
Maintainer: Yichen Wang <[email protected]>
License: GPL-3
Version: 0.1.99
Built: 2024-06-21 05:21:07 UTC
Source: https://github.com/welch-lab/CytoSimplex

Help Index


Normalize each column of the input matrix by the column sum

Description

Normalize each column of the input matrix by the column sum

Usage

colNormalize(x, scaleFactor = NULL, log = FALSE, ...)

## Default S3 method:
colNormalize(x, scaleFactor = NULL, log = FALSE, ...)

## S3 method for class 'dgCMatrix'
colNormalize(x, scaleFactor = NULL, log = FALSE, ...)

## S3 method for class 'Seurat'
colNormalize(
  x,
  scaleFactor = NULL,
  log = FALSE,
  assay = NULL,
  layer = "counts",
  ...
)

## S3 method for class 'SingleCellExperiment'
colNormalize(x, scaleFactor = NULL, log = FALSE, assay.type = "counts", ...)

Arguments

x

Feature by observation matrix. Alternatively, Seurat object or SingleCellExperiment object with raw counts available are also supported.

scaleFactor

Multiplier on normalized data. Default NULL.

log

Logical. Whether to take log1p transformation after scaling. Default FALSE

...

Additional arguments passed to methods

assay

For "Seurat" method, the specific assay to get data from. Default NULL to the default assay.

layer

For "Seurat" method, which layer of the assay to be used. Default "counts".

assay.type

For "SingleCellExperiment" method, the assay type to get data from. Default "counts".

Value

Normalized matrix of the same size

A Seurat object with normalized data in the specified slot of the specified assay.

A SingleCellExperiment object with normalized data in the specified assay. "normcounts" if log = FALSE and "logcounts" if log = TRUE.

Examples

rnaNorm <- colNormalize(rnaRaw)

# Seurat example
library(Seurat)
srt <- CreateSeuratObject(rnaRaw)
srt <- colNormalize(srt)


# SingleCellExperiment example
library(SingleCellExperiment)
sce <- SingleCellExperiment(assays = list(counts = rnaRaw))
sce <- colNormalize(sce)

Create binary plots

Description

Create binary plots that show similarity between single cells and two selected terminals in a barycentric coordinate. The two vertices are placed at the left and right of a 2D plot where x-axis measures the similarity. Y-axis is jittered for a clear view. A density (histogram) curve is added for indicating the distribution.

See plotTernary manual for more details.

Usage

plotBinary(x, ...)

## Default S3 method:
plotBinary(
  x,
  clusterVar,
  vertices,
  features = NULL,
  byCluster = NULL,
  processed = FALSE,
  method = c("euclidean", "cosine", "pearson", "spearman"),
  force = FALSE,
  sigma = 0.08,
  scale = TRUE,
  dotColor = "grey60",
  returnData = FALSE,
  ...
)

## S3 method for class 'Seurat'
plotBinary(
  x,
  layer = "counts",
  assay = NULL,
  clusterVar = NULL,
  processed = FALSE,
  ...
)

## S3 method for class 'SingleCellExperiment'
plotBinary(x, assay.type = "counts", clusterVar = NULL, processed = FALSE, ...)

## S3 method for class 'simMat'
plotBinary(
  x,
  dotSize = 0.6,
  dotColor = "grey60",
  densLinewidth = 0.8,
  labelColors = c("#3B4992FF", "#EE0000FF"),
  title = NULL,
  ...
)

Arguments

x

Input data. Can be a matrix or dgCMatrix object with cells as columns, a Seurat or SingleCellExperiment object. "simMat" method takes intermediate values.

...

Arguments passed to other methods.

clusterVar

A vector/factor assigning the cluster variable to each column of the matrix object. For "Seurat" method, NULL (default) for Idents(x), or a variable name in meta.data slot. For "SingleCellExperiment" method, NULL (default) for colLabels(x), or a variable name in colData slot.

vertices

Vector of three unique cluster names that will be used for plotting. Or a named list that groups clusters as three terminal vertices. There must not be any overlap between groups.

features

Valid matrix row subsetting index to select features for similarity calculation. Default NULL uses all available features.

byCluster

Default NULL to generate one plot with all cells. Set "all" to split cells in plot by cluster and returns a list of subplots for each cluster as well as the plot including all cells. Otherwise, a vector of cluster names to generate a list of subplots for the specified clusters.

processed

Logical. Whether the input matrix is already processed. TRUE will bypass internal preprocessing and input matrix will be directly used for similarity calculation. Default FALSE and raw count input is recommended. If missing in call, using slot = "counts" in "Seurat" method or using assay.type = "counts" in "SingleCellExperiment" method will force this argument to be FALSE and others for TRUE.

method

Similarity calculation method. Default "euclidean". Choose from "euclidean", "cosine", "pearson", "spearman".

force

Whether to force calculate the similarity when more then 500 features are detected, which is generally not recommended. Default FALSE.

sigma

Gaussian kernel parameter that controls the effect of variance. Only effective when using a distance metric (i.e. method is "euclidian" or "cosine"). Larger value tighten the dot spreading on figure. Default 0.08.

scale

Whether to min-max scale the distance matrix by clusters. Default TRUE.

returnData

Logical. Whether to return similarity data instead of generating plot. Default FALSE.

layer

For "Seurat" method, which layer of the assay to be used. Default "counts".

assay

For "Seurat" method, the specific assay to get data from. Default NULL to the default assay.

assay.type

For "SingleCellExperiment" methods. Which assay to use for calculating the similarity. Default "counts".

dotSize, dotColor

Dot aesthetics passed to geom_point. Default 0.6 and "grey60".

densLinewidth

Density plot line aesthetic. Default 0.8.

labelColors

Color of the axis lines and vertex labels. Default c("#3B4992FF", "#EE0000FF") (blue and red).

title

Title text of the plot. Default NULL.

Value

For 'simMat' method, a ggplot object. For other methods, a ggplot object when splitCluster = FALSE, or a list of ggplot objects when splitCluster = TRUE.

Examples

gene <- selectTopFeatures(rnaRaw, rnaCluster, c("RE", "OS"))
plotBinary(rnaRaw, rnaCluster, c("RE", "OS"), gene)

# Seurat example
library(Seurat)
srt <- CreateSeuratObject(rnaRaw)
Idents(srt) <- rnaCluster
gene <- selectTopFeatures(srt, vertices = c("OS", "RE"))
plotBinary(srt, features = gene, vertices = c("OS", "RE"))


# SingleCellExperiment example
library(SingleCellExperiment)
sce <- SingleCellExperiment(assays = list(counts = rnaRaw))
colLabels(sce) <- rnaCluster
gene <- selectTopFeatures(sce, vertices = c("OS", "RE"))
plotBinary(sce, features = gene, vertices = c("OS", "RE"))

Create quaternary simplex plots

Description

Create quaternary plots that show similarity between single cells and selected four terminals in a baricentric coordinate.

See plotTernary for more details on methodologies.

A dynamic rotating view in a GIF image file can be created with writeQuaternaryGIF. Package magick must be installed in advance. Linux users may refer to this installation guide.

Usage

plotQuaternary(x, ...)

## Default S3 method:
plotQuaternary(
  x,
  clusterVar,
  vertices,
  features = NULL,
  veloGraph = NULL,
  byCluster = NULL,
  processed = FALSE,
  method = c("euclidean", "cosine", "pearson", "spearman"),
  force = FALSE,
  sigma = 0.05,
  scale = TRUE,
  dotColorBy = NULL,
  dotColor = NULL,
  palette = "D",
  direction = 1,
  breaks = NULL,
  legendTitle = NULL,
  returnData = FALSE,
  ...
)

Arguments

x

Input data. Can be a matrix or dgCMatrix object with cells as columns, a Seurat or SingleCellExperiment object.

...

Arguments passed on to plotQuaternary.simMat

nGrid

Number of grids along the x-axis of the tetrahedron. Default 10.

radius

Arrow length of unit velocity. Lower this when arrows point outside of the tetrahedron. Default 0.2.

dotSize

Size of each dot. Default 0.6 for static figure, and 4 for interactive view.

labelColors

Colors of the vertex labels. Default c("#3B4992FF", "#EE0000FF", "#008B45FF", "#631879FF") (blue, red, green and purple).

arrowLinewidth

Arrow aesthetics. Default 1.6 for interactive view, 0.6 for static figure.

arrowAngle,arrowLen

Arrow aesthetics passed to TODOOOO grid::arrow. The length of the arrow will be internally converted to unit onject in inches. Default 20 and 0.1.

edgeLinewidth

Controls the linewidth of the edges of the tetrahedron. Default 1.

vertexLabelSize

Numeric, size of vertex text label relative to default size. Default 1.

title

Title text of the plot. Default NULL.

titleSize,titleColor

Setting on the main title text. Default 1, and "black".

theta,phi

Numeric scalar. The angles defining the viewing direction. theta gives the azimuthal direction and phi the colatitude. Default 20 and 0.

interactive

Logical. Whether to display plotly interactive view. Default TRUE.

clusterVar

A vector/factor assigning the cluster variable to each column of the matrix object. For "Seurat" method, NULL (default) for Idents(x), or a variable name in meta.data slot. For "SingleCellExperiment" method, NULL (default) for colLabels(x), or a variable name in colData slot.

vertices

Vector of three unique cluster names that will be used for plotting. Or a named list that groups clusters as three terminal vertices. There must not be any overlap between groups.

features

Valid matrix row subsetting index to select features for similarity calculation. Default NULL uses all available features.

veloGraph

Cell x cell dgCMatrix object containing velocity information. Shows velocity grid-arrow layer when specified. Default NULL does not show velocity.

byCluster

Default NULL to generate one plot with all cells. Set "all" to split cells in plot by cluster and returns a list of subplots for each cluster as well as the plot including all cells. Otherwise, a vector of cluster names to generate a list of subplots for the specified clusters.

processed

Logical. Whether the input matrix is already processed. TRUE will bypass internal preprocessing and input matrix will be directly used for similarity calculation. Default FALSE and raw count input is recommended. If missing in call, using slot = "counts" in "Seurat" method or using assay.type = "counts" in "SingleCellExperiment" method will force this argument to be FALSE and others for TRUE.

method

Similarity calculation method. Default "euclidean". Choose from "euclidean", "cosine", "pearson", "spearman".

force

Whether to force calculate the similarity when more then 500 features are detected, which is generally not recommended. Default FALSE.

sigma

Gaussian kernel parameter that controls the effect of variance. Only effective when using a distance metric (i.e. method is "euclidian" or "cosine"). Larger values tighten the dot spreading on figure. Default 0.05.

scale

Whether to min-max scale the distance matrix by clusters. Default TRUE.

dotColorBy

A vector/factor for coloring dots, can be either categorical (must be character or factor) or continuous. Default NULL.

dotColor

Character vector of color codes. When dotColorBy is NULL, use one or as many colors as the number of cells. If dotColorBy is categorical, specify as many colors as the number of categories in dotColorBy or ggplot2 categorical color palette is used by default. If dotColorBy is continuous, specify together with breaks argument.

palette

Color palette to use when dotColorBy is given. Default "D" (viridis) for continuous value and ggplot2 default for categorical value. See detail for alternatives.

direction

Sets the order of colors in the scale. Default 1 orders as palette default. If -1, the order of colors is reversed.

breaks

Number of breaks for continuous color scale passed to non-interactive "plot3D::scatter3D" call. Default NULL.

legendTitle

Title on the legend/colorbar. Default NULL uses "cluster" if dotColorBy is missing (default); user-end variable expression if dotColorBy is directly specified from plotQuaternary.default method; variable name if dotColorBy is specified from Seurat or SingleCellExperiment method.

returnData

Logical. Whether to return similarity and aggregated velocity data if applicable instead of generating plot. Default FALSE.

Value

By default, a "plotly" object. When interactive = FALSE, a "quatPlot" object when byCluster is not specified, or a "list" of "quatPlot" objects when byCluster is specified. When returnData = TRUE, a list of similarity matrix and aggregated velocity matrix is returned.

See Also

Other plotQuaternary: plotQuaternary.Seurat(), plotQuaternary.SingleCellExperiment()

Examples

gene <- selectTopFeatures(
    x = rnaRaw,
    clusterVar = rnaCluster,
    vertices = c("RE", "OS", "CH", "ORT")
)
plotQuaternary(
    x = rnaRaw,
    clusterVar = rnaCluster,
    vertices = c("RE", "OS", "CH", "ORT"),
    features = gene
)

Craete quaternary simplex plot with Seurat object

Description

Create quaternary plots that show similarity between single cells and selected four terminals in a baricentric coordinate.

See plotTernary for more details on methodologies.

A dynamic rotating view in a GIF image file can be created with writeQuaternaryGIF. Package magick must be installed in advance. Linux users may refer to this installation guide.

Usage

## S3 method for class 'Seurat'
plotQuaternary(
  x,
  layer = "counts",
  assay = NULL,
  clusterVar = NULL,
  processed = FALSE,
  dotColorBy = NULL,
  legendTitle = NULL,
  ...
)

Arguments

x

A Seurat object

layer

Layer in the specified assay to use. Default "counts".

assay

The assay to get data from. Default NULL uses the default assay.

clusterVar

A variable name in meta.data (x[[]]). Default NULL uses Idents(x).

processed

Logical. Whether the input matrix is already processed. TRUE will bypass internal preprocessing and input matrix will be directly used for similarity calculation. Default FALSE and raw count input is recommended. If missing in call, using slot = "counts" in "Seurat" method or using assay.type = "counts" in "SingleCellExperiment" method will force this argument to be FALSE and others for TRUE.

dotColorBy

A vector/factor for coloring dots, can be either categorical (must be character or factor) or continuous. Default NULL.

legendTitle

Title on the legend/colorbar. Default NULL uses "cluster" if dotColorBy is missing (default); user-end variable expression if dotColorBy is directly specified from plotQuaternary.default method; variable name if dotColorBy is specified from Seurat or SingleCellExperiment method.

...

Arguments passed on to plotQuaternary.default, plotQuaternary.simMat

vertices

Vector of three unique cluster names that will be used for plotting. Or a named list that groups clusters as three terminal vertices. There must not be any overlap between groups.

features

Valid matrix row subsetting index to select features for similarity calculation. Default NULL uses all available features.

byCluster

Default NULL to generate one plot with all cells. Set "all" to split cells in plot by cluster and returns a list of subplots for each cluster as well as the plot including all cells. Otherwise, a vector of cluster names to generate a list of subplots for the specified clusters.

veloGraph

Cell x cell dgCMatrix object containing velocity information. Shows velocity grid-arrow layer when specified. Default NULL does not show velocity.

method

Similarity calculation method. Default "euclidean". Choose from "euclidean", "cosine", "pearson", "spearman".

force

Whether to force calculate the similarity when more then 500 features are detected, which is generally not recommended. Default FALSE.

sigma

Gaussian kernel parameter that controls the effect of variance. Only effective when using a distance metric (i.e. method is "euclidian" or "cosine"). Larger values tighten the dot spreading on figure. Default 0.05.

scale

Whether to min-max scale the distance matrix by clusters. Default TRUE.

dotColor

Character vector of color codes. When dotColorBy is NULL, use one or as many colors as the number of cells. If dotColorBy is categorical, specify as many colors as the number of categories in dotColorBy or ggplot2 categorical color palette is used by default. If dotColorBy is continuous, specify together with breaks argument.

palette

Color palette to use when dotColorBy is given. Default "D" (viridis) for continuous value and ggplot2 default for categorical value. See detail for alternatives.

direction

Sets the order of colors in the scale. Default 1 orders as palette default. If -1, the order of colors is reversed.

breaks

Number of breaks for continuous color scale passed to non-interactive "plot3D::scatter3D" call. Default NULL.

returnData

Logical. Whether to return similarity and aggregated velocity data if applicable instead of generating plot. Default FALSE.

nGrid

Number of grids along the x-axis of the tetrahedron. Default 10.

radius

Arrow length of unit velocity. Lower this when arrows point outside of the tetrahedron. Default 0.2.

dotSize

Size of each dot. Default 0.6 for static figure, and 4 for interactive view.

labelColors

Colors of the vertex labels. Default c("#3B4992FF", "#EE0000FF", "#008B45FF", "#631879FF") (blue, red, green and purple).

arrowLinewidth

Arrow aesthetics. Default 1.6 for interactive view, 0.6 for static figure.

arrowAngle,arrowLen

Arrow aesthetics passed to TODOOOO grid::arrow. The length of the arrow will be internally converted to unit onject in inches. Default 20 and 0.1.

edgeLinewidth

Controls the linewidth of the edges of the tetrahedron. Default 1.

vertexLabelSize

Numeric, size of vertex text label relative to default size. Default 1.

title

Title text of the plot. Default NULL.

titleSize,titleColor

Setting on the main title text. Default 1, and "black".

theta,phi

Numeric scalar. The angles defining the viewing direction. theta gives the azimuthal direction and phi the colatitude. Default 20 and 0.

interactive

Logical. Whether to display plotly interactive view. Default TRUE.

Value

By default, a "plotly" object. When interactive = FALSE, a "quatPlot" object when byCluster is not specified, or a "list" of "quatPlot" objects when byCluster is specified. When returnData = TRUE, a list of similarity matrix and aggregated velocity matrix is returned.

See Also

Other plotQuaternary: plotQuaternary(), plotQuaternary.SingleCellExperiment()

Examples

# Seurat example
if (requireNamespace("Seurat", quietly = TRUE)) {
  require(Seurat)
  srt <- CreateSeuratObject(rnaRaw)
  Idents(srt) <- rnaCluster
  gene <- selectTopFeatures(srt, vertices = c("OS", "RE", "CH", "ORT"))
  plotQuaternary(srt, features = gene,
                 vertices = c("OS", "RE", "CH", "ORT"))
}

Create quaternary simplex plot with pre-calculated similarity matrix

Description

Create quaternary simplex plot with pre-calculated similarity matrix

Usage

## S3 method for class 'simMat'
plotQuaternary(
  x,
  veloMat = NULL,
  nGrid = 10,
  radius = 0.2,
  dotSize = NULL,
  colorArg = NULL,
  labelColors = c("#3B4992FF", "#EE0000FF", "#008B45FF", "#631879FF"),
  arrowLinewidth = NULL,
  arrowAngle = 20,
  arrowLen = 0.1,
  vertexLabelSize = NULL,
  edgeLinewidth = 1,
  title = NULL,
  titleSize = 1,
  titleColor = "black",
  theta = 20,
  phi = 0,
  interactive = TRUE,
  ...
)

Arguments

x

simMat object, n cells by 4 vertices, each row summing to 1.

veloMat

Aggregated velocity matrix. Output of aggrVeloGraph.

nGrid

Number of grids along the x-axis of the tetrahedron. Default 10.

radius

Arrow length of unit velocity. Lower this when arrows point outside of the tetrahedron. Default 0.2.

dotSize

Size of each dot. Default 0.6 for static figure, and 4 for interactive view.

colorArg

A "colorArg" object, internally prepared by plotQuaternary.default. Default NULL.

labelColors

Colors of the vertex labels. Default c("#3B4992FF", "#EE0000FF", "#008B45FF", "#631879FF") (blue, red, green and purple).

arrowLinewidth

Arrow aesthetics. Default 1.6 for interactive view, 0.6 for static figure.

arrowAngle, arrowLen

Arrow aesthetics passed to TODOOOO grid::arrow. The length of the arrow will be internally converted to unit onject in inches. Default 20 and 0.1.

vertexLabelSize

Numeric, size of vertex text label relative to default size. Default 1.

edgeLinewidth

Controls the linewidth of the edges of the tetrahedron. Default 1.

title

Title text of the plot. Default NULL.

titleSize, titleColor

Setting on the main title text. Default 1, and "black".

theta, phi

Numeric scalar. The angles defining the viewing direction. theta gives the azimuthal direction and phi the colatitude. Default 20 and 0.

interactive

Logical. Whether to display plotly interactive view. Default TRUE.

...

Not used

Value

A "quatPlot" object, can be displayed by printing.


Create quaternary simplex plot with SingleCellExperiment object

Description

Create quaternary plots that show similarity between single cells and selected four terminals in a baricentric coordinate.

See plotTernary for more details on methodologies.

A dynamic rotating view in a GIF image file can be created with writeQuaternaryGIF. Package magick must be installed in advance. Linux users may refer to this installation guide.

Usage

## S3 method for class 'SingleCellExperiment'
plotQuaternary(
  x,
  assay.type = "counts",
  clusterVar = NULL,
  processed = FALSE,
  dotColorBy = NULL,
  legendTitle = NULL,
  ...
)

Arguments

x

A SingleCellExperiment object

assay.type

Assay to use for calculating the similarity. Default "counts".

clusterVar

A variable name in colData(x). Default NULL uses colLabels(x).

processed

Logical. Whether the input matrix is already processed. TRUE will bypass internal preprocessing and input matrix will be directly used for similarity calculation. Default FALSE and raw count input is recommended. If missing in call, using slot = "counts" in "Seurat" method or using assay.type = "counts" in "SingleCellExperiment" method will force this argument to be FALSE and others for TRUE.

dotColorBy

A vector/factor for coloring dots, can be either categorical (must be character or factor) or continuous. Default NULL.

legendTitle

Title on the legend/colorbar. Default NULL uses "cluster" if dotColorBy is missing (default); user-end variable expression if dotColorBy is directly specified from plotQuaternary.default method; variable name if dotColorBy is specified from Seurat or SingleCellExperiment method.

...

Arguments passed on to plotQuaternary.default, plotQuaternary.simMat

vertices

Vector of three unique cluster names that will be used for plotting. Or a named list that groups clusters as three terminal vertices. There must not be any overlap between groups.

features

Valid matrix row subsetting index to select features for similarity calculation. Default NULL uses all available features.

byCluster

Default NULL to generate one plot with all cells. Set "all" to split cells in plot by cluster and returns a list of subplots for each cluster as well as the plot including all cells. Otherwise, a vector of cluster names to generate a list of subplots for the specified clusters.

veloGraph

Cell x cell dgCMatrix object containing velocity information. Shows velocity grid-arrow layer when specified. Default NULL does not show velocity.

method

Similarity calculation method. Default "euclidean". Choose from "euclidean", "cosine", "pearson", "spearman".

force

Whether to force calculate the similarity when more then 500 features are detected, which is generally not recommended. Default FALSE.

sigma

Gaussian kernel parameter that controls the effect of variance. Only effective when using a distance metric (i.e. method is "euclidian" or "cosine"). Larger values tighten the dot spreading on figure. Default 0.05.

scale

Whether to min-max scale the distance matrix by clusters. Default TRUE.

dotColor

Character vector of color codes. When dotColorBy is NULL, use one or as many colors as the number of cells. If dotColorBy is categorical, specify as many colors as the number of categories in dotColorBy or ggplot2 categorical color palette is used by default. If dotColorBy is continuous, specify together with breaks argument.

palette

Color palette to use when dotColorBy is given. Default "D" (viridis) for continuous value and ggplot2 default for categorical value. See detail for alternatives.

direction

Sets the order of colors in the scale. Default 1 orders as palette default. If -1, the order of colors is reversed.

breaks

Number of breaks for continuous color scale passed to non-interactive "plot3D::scatter3D" call. Default NULL.

returnData

Logical. Whether to return similarity and aggregated velocity data if applicable instead of generating plot. Default FALSE.

nGrid

Number of grids along the x-axis of the tetrahedron. Default 10.

radius

Arrow length of unit velocity. Lower this when arrows point outside of the tetrahedron. Default 0.2.

dotSize

Size of each dot. Default 0.6 for static figure, and 4 for interactive view.

labelColors

Colors of the vertex labels. Default c("#3B4992FF", "#EE0000FF", "#008B45FF", "#631879FF") (blue, red, green and purple).

arrowLinewidth

Arrow aesthetics. Default 1.6 for interactive view, 0.6 for static figure.

arrowAngle,arrowLen

Arrow aesthetics passed to TODOOOO grid::arrow. The length of the arrow will be internally converted to unit onject in inches. Default 20 and 0.1.

edgeLinewidth

Controls the linewidth of the edges of the tetrahedron. Default 1.

vertexLabelSize

Numeric, size of vertex text label relative to default size. Default 1.

title

Title text of the plot. Default NULL.

titleSize,titleColor

Setting on the main title text. Default 1, and "black".

theta,phi

Numeric scalar. The angles defining the viewing direction. theta gives the azimuthal direction and phi the colatitude. Default 20 and 0.

interactive

Logical. Whether to display plotly interactive view. Default TRUE.

Value

By default, a "plotly" object. When interactive = FALSE, a "quatPlot" object when byCluster is not specified, or a "list" of "quatPlot" objects when byCluster is specified. When returnData = TRUE, a list of similarity matrix and aggregated velocity matrix is returned.

See Also

Other plotQuaternary: plotQuaternary(), plotQuaternary.Seurat()

Examples

# SingleCellExperiment example
if (requreNamespace("SingleCellExperiment", quietly = TRUE)) {
  require(SingleCellExperiment)
  sce <- SingleCellExperiment(assays = list(counts = rnaRaw))
  colLabels(sce) <- rnaCluster
  gene <- selectTopFeatures(sce, vertices = c("OS", "RE", "CH", "ORT"))
  plotQuaternary(sce, features = gene,
                 vertices = c("OS", "RE", "CH", "ORT"))
}

Create ternary simplex plots

Description

Create ternary plots that show similarity between single cells and selected three terminals in a ternary baricentric coordinate.

Usage

plotTernary(x, ...)

## Default S3 method:
plotTernary(
  x,
  clusterVar,
  vertices,
  features = NULL,
  veloGraph = NULL,
  byCluster = NULL,
  processed = FALSE,
  method = c("euclidean", "cosine", "pearson", "spearman"),
  force = FALSE,
  sigma = 0.08,
  scale = TRUE,
  dotColorBy = NULL,
  dotColor = NULL,
  palette = "D",
  direction = 1,
  breaks = NULL,
  legendTitle = NULL,
  returnData = FALSE,
  ...
)

Arguments

x

Input data. Can be a matrix or dgCMatrix object with cells as columns, a Seurat or SingleCellExperiment object. "simMat" method takes intermediate values.

...

Arguments passed on to plotTernary.simMat

title

Title text of the plot. Default NULL.

nGrid

Number of grids along the bottom side of the equilateral triangle. Default 10.

radius

Arrow length of unit velocity. Lower this when arrows point outside of the coordinate. Default 0.1.

dotSize

Dot aesthetics passed to geom_point. Default 0.6 when not interactive, 4 when interactive.

dotShuffle

Whether to shuffle the order of dots being added to the plot, useful when categorical colors are used and mixing of categories is expected. Default NULL does shuffle when dotColorBy given is categorical and does not otherwise.

labelColors

Colors of the axis lines and vertex labels. Default c("#3B4992FF", "#EE0000FF", "#008B45FF") (blue, red and green)

vertexLabelSize

Size of vertex labels. Default 6 when not interactive, 16 when interactive.

vertexLabelDrift

Position adjustment of the vertex labels, only applied to non-interactive view. Default 0.03.

axisBreak

Number of breaks to be labeled along axis. Default 5.

axisTextShow

Logical, whether to show axis text. Default TRUE.

axisTextSize

Size of text along each axis break. Default 4 for non-interactive view, 12 for interactive view.

axisTextDrift

Position adjustment of the axis text, only applied to non-interactive view. Default 0.01.

gridLineAlpha

Transparency of background grid lines. Default 0.6.

arrowLinewidth

Line width of the velocity arrows. Default 0.25 for non-interactive view, 2 for interactive view.

arrowAngle

Controls the angle of the arrowhead, only applied to non-interactive view. Default 20.

arrowLen

Control length in centimetre from arrow tip to arrow tail, only applied to non-interactive view. Default 0.2.

titleSize

Size of title text. Default 14 for non-interactive view, 20 for interactive view.

equilateral

Logical, whether to always display the triangle as equilateral. Default TRUE.

margin

Margin allowed around of the triangle plotting region when equilateral = TRUE

interactive

Logical. Whether to display plotly interactive view. Default FALSE.

clusterVar

A vector/factor assigning the cluster variable to each column of the matrix object. For "Seurat" method, NULL (default) for Idents(x), or a variable name in meta.data slot. For "SingleCellExperiment" method, NULL (default) for colLabels(x), or a variable name in colData slot.

vertices

Vector of three unique cluster names that will be used for plotting. Or a named list that groups clusters as three terminal vertices. There must not be any overlap between groups.

features

Valid matrix row subsetting index to select features for similarity calculation. Default NULL uses all available features.

veloGraph

Cell x cell dgCMatrix object containing velocity information. Shows velocity grid-arrow layer when specified. Default NULL does not show velocity.

byCluster

Default NULL to generate one plot with all cells. Set "all" to split cells in plot by cluster and returns a list of subplots for each cluster as well as the plot including all cells. Otherwise, a vector of cluster names to generate a list of subplots for the specified clusters.

processed

Logical. Whether the input matrix is already processed. TRUE will bypass internal preprocessing and input matrix will be directly used for similarity calculation. Default FALSE and raw count input is recommended. If missing in call, using slot = "counts" in "Seurat" method or using assay.type = "counts" in "SingleCellExperiment" method will force this argument to be FALSE and others for TRUE.

method

Similarity calculation method. Default "euclidean". Choose from "euclidean", "cosine", "pearson", "spearman".

force

Whether to force calculate the similarity when more then 500 features are detected, which is generally not recommended. Default FALSE.

sigma

Gaussian kernel parameter that controls the effect of variance. Only effective when using a distance metric (i.e. method is "euclidian" or "cosine"). Larger values tighten the dot spreading on figure. Default 0.08.

scale

Whether to min-max scale the distance matrix by clusters. Default TRUE.

dotColorBy

A vector/factor for coloring dots, can be either categorical (must be character or factor) or continuous. Default NULL.

dotColor

Character vector of color codes. When dotColorBy is NULL, use one or as many colors as the number of cells. If dotColorBy is categorical, specify as many colors as the number of categories in dotColorBy or ggplot2 categorical color palette is used by default. If dotColorBy is continuous, specify together with breaks argument.

palette

Color palette to use when dotColorBy is given. Default "D" (viridis) for continuous value and ggplot2 default for categorical value. See detail for alternatives.

direction

Sets the order of colors in the scale. Default 1 orders as palette default. If -1, the order of colors is reversed.

breaks

Number of breaks for continuous color scale passed to non-interactive "plot3D::scatter3D" call. Default NULL.

legendTitle

Title on the legend/colorbar. Default NULL uses "cluster" if dotColorBy is missing (default); user-end variable expression if dotColorBy is directly specified from plotQuaternary.default method; variable name if dotColorBy is specified from Seurat or SingleCellExperiment method.

returnData

Logical. Whether to return similarity and aggregated velocity data if applicable instead of generating plot. Default FALSE.

Details

Argument inheritance - For matrix/dgCMatrix ("default" method), we first calculate the similarity matrix and obtain a "simMat" object. Then the "simMat" method is internally called. For data container objects (e.g. Seurat), we obtain the correct data matrix first and then call the "default" method. The arguments inherits as the flow described above.

The calculation of similarity matrix - The similarity is calculated either by converting a distance metric ("euclidean" or "cosine") with Gaussian kernel, or directly computed with correlation metrics ("pearson" or "spearman"). The centroid of each terminal is obtained first, and the specified metric from each cell to each terminal is calculated. The similarity matrix (n cells by v terminals) is lastly normalized to sum to 1 for each cell, so it becomes a baricentric coordinate.

Value

By default, a "ggplot" object when byCluster is not specified, a list of "ggplot" object when byCluster is specified. When interactive = TRUE, a "plotly" object is returned. When returnData = TRUE, a list of similarity matrix and aggregated velocity matrix is returned.

See Also

Other plotTernary: plotTernary.Seurat(), plotTernary.SingleCellExperiment()

Examples

gene <- selectTopFeatures(rnaRaw, rnaCluster, c("OS", "RE", "CH"))
plotTernary(rnaRaw, rnaCluster, c("OS", "RE", "CH"), gene)

Create ternary simplex plot with Seurat objects

Description

Create ternary plots that show similarity between single cells and selected three terminals in a ternary baricentric coordinate.

Usage

## S3 method for class 'Seurat'
plotTernary(
  x,
  layer = "counts",
  assay = NULL,
  clusterVar = NULL,
  processed = FALSE,
  dotColorBy = NULL,
  legendTitle = NULL,
  ...
)

Arguments

x

A Seurat object

layer

Layer in the specified assay to use. Default "counts".

assay

The assay to get data from. Default NULL uses the default assay.

clusterVar

A variable name in meta.data (x[[]]). Default NULL uses Idents(x).

processed

Logical. Whether the input matrix is already processed. TRUE will bypass internal preprocessing and input matrix will be directly used for similarity calculation. Default FALSE and raw count input is recommended. If missing in call, using slot = "counts" in "Seurat" method or using assay.type = "counts" in "SingleCellExperiment" method will force this argument to be FALSE and others for TRUE.

dotColorBy

A vector/factor for coloring dots, can be either categorical (must be character or factor) or continuous. Default NULL.

legendTitle

Title on the legend/colorbar. Default NULL uses "cluster" if dotColorBy is missing (default); user-end variable expression if dotColorBy is directly specified from plotQuaternary.default method; variable name if dotColorBy is specified from Seurat or SingleCellExperiment method.

...

Arguments passed on to plotTernary.default, plotTernary.simMat

vertices

Vector of three unique cluster names that will be used for plotting. Or a named list that groups clusters as three terminal vertices. There must not be any overlap between groups.

features

Valid matrix row subsetting index to select features for similarity calculation. Default NULL uses all available features.

byCluster

Default NULL to generate one plot with all cells. Set "all" to split cells in plot by cluster and returns a list of subplots for each cluster as well as the plot including all cells. Otherwise, a vector of cluster names to generate a list of subplots for the specified clusters.

veloGraph

Cell x cell dgCMatrix object containing velocity information. Shows velocity grid-arrow layer when specified. Default NULL does not show velocity.

method

Similarity calculation method. Default "euclidean". Choose from "euclidean", "cosine", "pearson", "spearman".

force

Whether to force calculate the similarity when more then 500 features are detected, which is generally not recommended. Default FALSE.

sigma

Gaussian kernel parameter that controls the effect of variance. Only effective when using a distance metric (i.e. method is "euclidian" or "cosine"). Larger values tighten the dot spreading on figure. Default 0.08.

scale

Whether to min-max scale the distance matrix by clusters. Default TRUE.

dotColor

Character vector of color codes. When dotColorBy is NULL, use one or as many colors as the number of cells. If dotColorBy is categorical, specify as many colors as the number of categories in dotColorBy or ggplot2 categorical color palette is used by default. If dotColorBy is continuous, specify together with breaks argument.

palette

Color palette to use when dotColorBy is given. Default "D" (viridis) for continuous value and ggplot2 default for categorical value. See detail for alternatives.

direction

Sets the order of colors in the scale. Default 1 orders as palette default. If -1, the order of colors is reversed.

breaks

Number of breaks for continuous color scale passed to non-interactive "plot3D::scatter3D" call. Default NULL.

returnData

Logical. Whether to return similarity and aggregated velocity data if applicable instead of generating plot. Default FALSE.

title

Title text of the plot. Default NULL.

nGrid

Number of grids along the bottom side of the equilateral triangle. Default 10.

radius

Arrow length of unit velocity. Lower this when arrows point outside of the coordinate. Default 0.1.

dotSize

Dot aesthetics passed to geom_point. Default 0.6 when not interactive, 4 when interactive.

dotShuffle

Whether to shuffle the order of dots being added to the plot, useful when categorical colors are used and mixing of categories is expected. Default NULL does shuffle when dotColorBy given is categorical and does not otherwise.

labelColors

Colors of the axis lines and vertex labels. Default c("#3B4992FF", "#EE0000FF", "#008B45FF") (blue, red and green)

vertexLabelSize

Size of vertex labels. Default 6 when not interactive, 16 when interactive.

vertexLabelDrift

Position adjustment of the vertex labels, only applied to non-interactive view. Default 0.03.

axisBreak

Number of breaks to be labeled along axis. Default 5.

axisTextShow

Logical, whether to show axis text. Default TRUE.

axisTextSize

Size of text along each axis break. Default 4 for non-interactive view, 12 for interactive view.

axisTextDrift

Position adjustment of the axis text, only applied to non-interactive view. Default 0.01.

gridLineAlpha

Transparency of background grid lines. Default 0.6.

arrowLinewidth

Line width of the velocity arrows. Default 0.25 for non-interactive view, 2 for interactive view.

arrowAngle

Controls the angle of the arrowhead, only applied to non-interactive view. Default 20.

arrowLen

Control length in centimetre from arrow tip to arrow tail, only applied to non-interactive view. Default 0.2.

titleSize

Size of title text. Default 14 for non-interactive view, 20 for interactive view.

equilateral

Logical, whether to always display the triangle as equilateral. Default TRUE.

margin

Margin allowed around of the triangle plotting region when equilateral = TRUE

interactive

Logical. Whether to display plotly interactive view. Default FALSE.

Value

By default, a "ggplot" object when byCluster is not specified, a list of "ggplot" object when byCluster is specified. When interactive = TRUE, a "plotly" object is returned. When returnData = TRUE, a list of similarity matrix and aggregated velocity matrix is returned.

See Also

Other plotTernary: plotTernary(), plotTernary.SingleCellExperiment()

Examples

# Seurat example
library(Seurat)
srt <- CreateSeuratObject(rnaRaw)
Idents(srt) <- rnaCluster
gene <- selectTopFeatures(srt, vertices = c("OS", "RE", "CH"))
plotTernary(srt, features = gene, vertices = c("OS", "RE", "CH"))

Create quaternary simplex plot with pre-calculated similarity matrix

Description

Create quaternary simplex plot with pre-calculated similarity matrix

Usage

## S3 method for class 'simMat'
plotTernary(
  x,
  title = NULL,
  veloMat = NULL,
  nGrid = 10,
  radius = 0.1,
  dotSize = NULL,
  dotShuffle = NULL,
  colorArg = NULL,
  labelColors = c("#3B4992FF", "#EE0000FF", "#008B45FF"),
  vertexLabelSize = NULL,
  vertexLabelDrift = 0.03,
  axisBreak = 5,
  axisTextShow = TRUE,
  axisTextSize = NULL,
  axisTextDrift = 0.01,
  gridLineAlpha = 0.6,
  arrowLinewidth = NULL,
  arrowAngle = 20,
  arrowLen = 0.2,
  titleSize = NULL,
  equilateral = TRUE,
  margin = 0.1,
  interactive = FALSE,
  ...
)

Arguments

x

simMat object, n cells by 4 vertices, each row summing to 1.

title

Title text of the plot. Default NULL.

veloMat

Aggregated velocity matrix. Output of aggrVeloGraph.

nGrid

Number of grids along the bottom side of the equilateral triangle. Default 10.

radius

Arrow length of unit velocity. Lower this when arrows point outside of the coordinate. Default 0.1.

dotSize

Dot aesthetics passed to geom_point. Default 0.6 when not interactive, 4 when interactive.

dotShuffle

Whether to shuffle the order of dots being added to the plot, useful when categorical colors are used and mixing of categories is expected. Default NULL does shuffle when dotColorBy given is categorical and does not otherwise.

colorArg

A "colorArg" object, internally prepared by plotQuaternary.default. Default NULL.

labelColors

Colors of the axis lines and vertex labels. Default c("#3B4992FF", "#EE0000FF", "#008B45FF") (blue, red and green)

vertexLabelSize

Size of vertex labels. Default 6 when not interactive, 16 when interactive.

vertexLabelDrift

Position adjustment of the vertex labels, only applied to non-interactive view. Default 0.03.

axisBreak

Number of breaks to be labeled along axis. Default 5.

axisTextShow

Logical, whether to show axis text. Default TRUE.

axisTextSize

Size of text along each axis break. Default 4 for non-interactive view, 12 for interactive view.

axisTextDrift

Position adjustment of the axis text, only applied to non-interactive view. Default 0.01.

gridLineAlpha

Transparency of background grid lines. Default 0.6.

arrowLinewidth

Line width of the velocity arrows. Default 0.25 for non-interactive view, 2 for interactive view.

arrowAngle

Controls the angle of the arrowhead, only applied to non-interactive view. Default 20.

arrowLen

Control length in centimetre from arrow tip to arrow tail, only applied to non-interactive view. Default 0.2.

titleSize

Size of title text. Default 14 for non-interactive view, 20 for interactive view.

equilateral

Logical, whether to always display the triangle as equilateral. Default TRUE.

margin

Margin allowed around of the triangle plotting region when equilateral = TRUE

interactive

Logical. Whether to display plotly interactive view. Default FALSE.

...

Not used


Create ternary simplex plot with SingleCellExperiment objects

Description

Create ternary plots that show similarity between single cells and selected three terminals in a ternary baricentric coordinate.

Usage

## S3 method for class 'SingleCellExperiment'
plotTernary(
  x,
  assay.type = "counts",
  clusterVar = NULL,
  processed = FALSE,
  dotColorBy = NULL,
  legendTitle = NULL,
  ...
)

Arguments

x

A SingleCellExperiment object.

assay.type

Assay to use for calculating the similarity. Default "counts".

clusterVar

A variable name in colData(x). Default NULL uses colLabels(x).

processed

Logical. Whether the input matrix is already processed. TRUE will bypass internal preprocessing and input matrix will be directly used for similarity calculation. Default FALSE and raw count input is recommended. If missing in call, using slot = "counts" in "Seurat" method or using assay.type = "counts" in "SingleCellExperiment" method will force this argument to be FALSE and others for TRUE.

dotColorBy

A vector/factor for coloring dots, can be either categorical (must be character or factor) or continuous. Default NULL.

legendTitle

Title on the legend/colorbar. Default NULL uses "cluster" if dotColorBy is missing (default); user-end variable expression if dotColorBy is directly specified from plotQuaternary.default method; variable name if dotColorBy is specified from Seurat or SingleCellExperiment method.

...

Arguments passed on to plotTernary.default, plotTernary.simMat

vertices

Vector of three unique cluster names that will be used for plotting. Or a named list that groups clusters as three terminal vertices. There must not be any overlap between groups.

features

Valid matrix row subsetting index to select features for similarity calculation. Default NULL uses all available features.

byCluster

Default NULL to generate one plot with all cells. Set "all" to split cells in plot by cluster and returns a list of subplots for each cluster as well as the plot including all cells. Otherwise, a vector of cluster names to generate a list of subplots for the specified clusters.

veloGraph

Cell x cell dgCMatrix object containing velocity information. Shows velocity grid-arrow layer when specified. Default NULL does not show velocity.

method

Similarity calculation method. Default "euclidean". Choose from "euclidean", "cosine", "pearson", "spearman".

force

Whether to force calculate the similarity when more then 500 features are detected, which is generally not recommended. Default FALSE.

sigma

Gaussian kernel parameter that controls the effect of variance. Only effective when using a distance metric (i.e. method is "euclidian" or "cosine"). Larger values tighten the dot spreading on figure. Default 0.08.

scale

Whether to min-max scale the distance matrix by clusters. Default TRUE.

dotColor

Character vector of color codes. When dotColorBy is NULL, use one or as many colors as the number of cells. If dotColorBy is categorical, specify as many colors as the number of categories in dotColorBy or ggplot2 categorical color palette is used by default. If dotColorBy is continuous, specify together with breaks argument.

palette

Color palette to use when dotColorBy is given. Default "D" (viridis) for continuous value and ggplot2 default for categorical value. See detail for alternatives.

direction

Sets the order of colors in the scale. Default 1 orders as palette default. If -1, the order of colors is reversed.

breaks

Number of breaks for continuous color scale passed to non-interactive "plot3D::scatter3D" call. Default NULL.

returnData

Logical. Whether to return similarity and aggregated velocity data if applicable instead of generating plot. Default FALSE.

title

Title text of the plot. Default NULL.

nGrid

Number of grids along the bottom side of the equilateral triangle. Default 10.

radius

Arrow length of unit velocity. Lower this when arrows point outside of the coordinate. Default 0.1.

dotSize

Dot aesthetics passed to geom_point. Default 0.6 when not interactive, 4 when interactive.

dotShuffle

Whether to shuffle the order of dots being added to the plot, useful when categorical colors are used and mixing of categories is expected. Default NULL does shuffle when dotColorBy given is categorical and does not otherwise.

labelColors

Colors of the axis lines and vertex labels. Default c("#3B4992FF", "#EE0000FF", "#008B45FF") (blue, red and green)

vertexLabelSize

Size of vertex labels. Default 6 when not interactive, 16 when interactive.

vertexLabelDrift

Position adjustment of the vertex labels, only applied to non-interactive view. Default 0.03.

axisBreak

Number of breaks to be labeled along axis. Default 5.

axisTextShow

Logical, whether to show axis text. Default TRUE.

axisTextSize

Size of text along each axis break. Default 4 for non-interactive view, 12 for interactive view.

axisTextDrift

Position adjustment of the axis text, only applied to non-interactive view. Default 0.01.

gridLineAlpha

Transparency of background grid lines. Default 0.6.

arrowLinewidth

Line width of the velocity arrows. Default 0.25 for non-interactive view, 2 for interactive view.

arrowAngle

Controls the angle of the arrowhead, only applied to non-interactive view. Default 20.

arrowLen

Control length in centimetre from arrow tip to arrow tail, only applied to non-interactive view. Default 0.2.

titleSize

Size of title text. Default 14 for non-interactive view, 20 for interactive view.

equilateral

Logical, whether to always display the triangle as equilateral. Default TRUE.

margin

Margin allowed around of the triangle plotting region when equilateral = TRUE

interactive

Logical. Whether to display plotly interactive view. Default FALSE.

Value

By default, a "ggplot" object when byCluster is not specified, a list of "ggplot" object when byCluster is specified. When interactive = TRUE, a "plotly" object is returned. When returnData = TRUE, a list of similarity matrix and aggregated velocity matrix is returned.

See Also

Other plotTernary: plotTernary(), plotTernary.Seurat()

Examples

# SingleCellExperiment example
library(SingleCellExperiment)
sce <- SingleCellExperiment(assays = list(counts = rnaRaw))
colLabels(sce) <- rnaCluster
gene <- selectTopFeatures(sce, vertices = c("OS", "RE", "CH"))
plotTernary(sce, features = gene, vertices = c("OS", "RE", "CH"))

Extract 'adata.obs_names' from an H5AD file

Description

It frequently happens that velocity analyses stored in H5AD files do not contain the full raw count data suggested for CytoSimplex visualization. Extracting the cell IDs (e.g. barcodes) helps matching the velocity data to raw count data imported from other sources.

Usage

readH5ADObsNames(filename)

Arguments

filename

File path to the H5AD file.

Value

A character vector of cell IDs.

See Also

Other H5AD-reader: readH5ADObsVar(), readH5ADUnsSpMat(), readVelocytoLoom()

Examples

## Not run: 
h5adFile <- "path/to/analysis.h5ad"
cellIDs <- readH5ADObsNames(h5adFile)

## End(Not run)

Extract a variable from adata.obs stored in an H5AD file

Description

Primarily designed for fetching the annotation used for visualization.

Usage

readH5ADObsVar(filename, obsKey, named = TRUE, categoricalAsFactor = TRUE)

Arguments

filename

File path to the H5AD file.

obsKey

The variable name to extract, must use only one character string.

named

Logical, whether to name the vector with cell IDs that came from adata.obs_names. Default TRUE.

categoricalAsFactor

Logical, whether to convert categorical variables to factors. Default TRUE.

Value

A vector of the extracted variable, or a factor if the variable is encoded to be categorical and categoricalAsFactor = TRUE.

See Also

Other H5AD-reader: readH5ADObsNames(), readH5ADUnsSpMat(), readVelocytoLoom()

Examples

## Not run: 
h5adFile <- "path/to/analysis.h5ad"
cluster <- readH5ADObsVar(h5adFile, "leiden")

## End(Not run)

Extract a sparse matrix from adata.uns stored in an H5AD file

Description

Primarily designed for fetching the velocity data presented as a cell-cell transition graph.

Usage

readH5ADUnsSpMat(filename, unsKey)

Arguments

filename

File path to the H5AD file.

unsKey

The adata.uns key to extract, must use only one character string.

Value

A CSC-matrix of "dgCMatrix" class

See Also

Other H5AD-reader: readH5ADObsNames(), readH5ADObsVar(), readVelocytoLoom()

Examples

## Not run: 
h5adFile <- "path/to/analysis.h5ad"
velo <- readH5ADUnsSpMat(h5adFile, "velo_s_norm_graph")

## End(Not run)

Extract the raw counts from a LOOM file

Description

This function is primarily designed for fetching the raw count data from a LOOM file, output by Velocyto. We by default use the spliced counts.

Usage

readVelocytoLoom(
  filename,
  matrixPath = "layers/spliced",
  cellID = "CellID",
  featureID = "Gene",
  chunkSize = 1000
)

Arguments

filename

File path to the LOOM file.

matrixPath

A path in the LOOM file to the matrix to extract, following the inner HDF5 structure. Default "layers/spliced". See Details.

cellID

The name of the cell ID column in the LOOM column-attributes. The same thing as argument obs_names of scanpy.read_loom. Default "CellID".

featureID

The name of the feature ID column in the LOOM row-attributes. The same thing as argument var_names of scanpy.read_loom. Default "Gene".

chunkSize

The maximum size of the chunk to load the matrix. Default 1000.

Details

The velocyto output LOOM file is HDF5 based and is roughly organized as follows:

  • "matrix": The whole raw counts, which is the sum of spliced, unspliced and ambiguous counts.

  • layers: A group like a folder

    • "layers/spliced": The spliced counts.

    • "layers/unspliced": The unspliced counts.

    • "layers/ambiguous": The ambiguous counts.

An AnnData object created with Scanpy by default loads the data with a different structure, so that all the four matrices are accessible in adata.layers and set one of them (by default "layers/spliced") to adata.X.

Value

A sparse matrix of class "dgCMatrix", with cells as columns and genes as rows.

See Also

Other H5AD-reader: readH5ADObsNames(), readH5ADObsVar(), readH5ADUnsSpMat()

Examples

## Not run: 
loomFile <- "velocyto/out/analysis.loom"
rawCounts <- readVelocytoLoom(loomFile)

## End(Not run)

Major cell type annotation of the example mouse bone marrow data

Description

Major cell type annotation of the example mouse bone marrow data

Usage

rnaCluster

Format

factor object

Source

https://www.nature.com/articles/s41467-023-38034-2

References

Matsushita, Y., Liu, J., Chu, A.K.Y. et al. Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis. Nat Commun 14, 2383 (2023).


Mouse bone marrow scRNAseq example data

Description

Mouse bone marrow scRNAseq example data

Usage

rnaRaw

Format

dgCMatrix object

Source

https://www.nature.com/articles/s41467-023-38034-2

References

Matsushita, Y., Liu, J., Chu, A.K.Y. et al. Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis. Nat Commun 14, 2383 (2023).


Velocity graph of the example mouse bone marrow data

Description

Velocity graph of the example mouse bone marrow data

Usage

rnaVelo

Format

dgCMatrix object

Source

https://www.nature.com/articles/s41467-023-38034-2

References

Matsushita, Y., Liu, J., Chu, A.K.Y. et al. Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis. Nat Commun 14, 2383 (2023).


Pick top differentially presented features for similarity calculation

Description

Performs wilcoxon rank-sum test on input matrix. While clusterVar and vertices together defines the groups of cells to be set as terminals of the simplex, this function will test each of these groups against the rest of the cells. The U-Statistics (statistic), p-value (pval) and adjusted p-value (padj), together with average presence in group (avgExpr), log fold-change (logFC), AUC (auc), percentage in group (pct_in) and percentage out of group (pct_out) will be calculated. Set returnStats = TRUE to return the full statistics table.

Top features are selected by sorting primarily on adjusted p-value, and secondarily on log fold-change, after filtering for up-regulated features.

Usage

selectTopFeatures(x, clusterVar, vertices, ...)

## Default S3 method:
selectTopFeatures(
  x,
  clusterVar,
  vertices,
  nTop = 30,
  processed = FALSE,
  lfcThresh = 0.1,
  returnStats = FALSE,
  ...
)

## S3 method for class 'Seurat'
selectTopFeatures(
  x,
  clusterVar = NULL,
  vertices,
  assay = NULL,
  layer = "counts",
  processed = FALSE,
  ...
)

## S3 method for class 'SingleCellExperiment'
selectTopFeatures(
  x,
  clusterVar = NULL,
  vertices,
  assay.type = "counts",
  processed = FALSE,
  ...
)

Arguments

x

Dense or sparse matrix, observation per column. Preferrably a raw count matrix. Alternatively, a Seurat object or a SingleCellExperiment object.

clusterVar

A vector/factor assigning the cluster variable to each column of the matrix object. For "Seurat" method, NULL (default) for Idents(x), or a variable name in meta.data slot. For "SingleCellExperiment" method, NULL (default) for colLabels(x), or a variable name in colData slot.

vertices

Vector of cluster names that will be used for plotting. Or a named list that groups clusters as a terminal vertex. There must not be any overlap between groups.

...

Arguments passed to methods.

nTop

Number of top differentially presented features per terminal. Default 30.

processed

Logical. Whether the input matrix is already processed. TRUE will bypass internal preprocessing and input matrix will be directly used for rank-sum calculation. Default FALSE and raw count input is recommended.

lfcThresh

Threshold on log fold-change to identify up-regulated features. Default 0.1.

returnStats

Logical. Whether to return the full statistics table rather then returning the selected genes. Default FALSE

assay

Assay name of the Seurat object to be used. Default NULL.

layer

For "Seurat" method, which layer of the assay to be used. Default "counts".

assay.type

Assay name of the SingleCellExperiment object to be used. Default "counts".

Value

When returnStats = FALSE (default), a character vector of at most length(unique(vertices))*nTop feature names. When returnStats = TRUE, a data.frame of wilcoxon rank sum test statistics.

Examples

selectTopFeatures(rnaRaw, rnaCluster, c("OS", "RE"))

# Seurat example
library(Seurat)
srt <- CreateSeuratObject(rnaRaw)
Idents(srt) <- rnaCluster
gene <- selectTopFeatures(srt, vertices = c("OS", "RE"))


# SingleCellExperiment example
library(SingleCellExperiment)
sce <- SingleCellExperiment(assays = list(counts = rnaRaw))
colLabels(sce) <- rnaCluster
gene <- selectTopFeatures(sce, vertices = c("OS", "RE"))

Create GIF image for dynamic rotating view of 3D quaternary simplex plot

Description

Create GIF image for dynamic rotating view of 3D quaternary simplex plot

Usage

writeQuaternaryGIF(
  x,
  ...,
  cluster = NULL,
  filename = NULL,
  fps = 10,
  degreePerFrame = 10,
  width = 5,
  height = 5,
  res = 100
)

Arguments

x

Input object that plotQuaternary accepts.

...

All other arguments needed for plotQuaternary. Must be specified with exact argument names instead of a positional manner.

cluster

One cluster that exists in clusterVar if users need to view the plot for a specific group. Default NULL plot all cells.

filename

Output GIF image file path. Default NULL does not write to file.

fps

Number of frame per second, must be a factor of 100. Default 10.

degreePerFrame

Number of degree that the tetrahedron is rotated per frame. Default 10.

width, height, res

grDevices::png parameters to set figure size and resolutation. Width and Height are in inches. Default 5, 5, 100.

Value

A object of class magick-image that can be shown in the Viewer panel in RStudio or equivalent display device. If filename is specified, the GIF image will be written to the file path.

Examples

gene <- selectTopFeatures(rnaRaw, rnaCluster, c("RE", "OS", "CH", "ORT"))

writeQuaternaryGIF(rnaRaw, clusterVar = rnaCluster, features = gene,
                   vertices = c("RE", "OS", "CH", "ORT"),
                   gifPath = tempfile(fileext = ".gif"))