Type: Package
Title: A Versatile Visualization Suite
Version: 0.2.5
Description: A visualization suite primarily designed for single-cell RNA-sequencing data analysis applications, but adaptable to other purposes as well. It introduces novel plots to represent two-variable and frequency data and optimizes some commonly used plotting options (e.g., correlation, network, density and alluvial plots) for ease of usage and flexibility.
License: MIT + file LICENSE
Imports: abdiv, dplyr, ggalluvial, ggeasy, ggforce, ggraph, ggnewscale, ggplot2, ggrepel, grDevices, liver, methods, reshape2, rlang, stats, tidygraph, viridis
Encoding: UTF-8
RoxygenNote: 7.3.2
Suggests: testthat (≥ 3.0.0)
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2025-09-14 00:56:56 UTC; Andrei
Author: Andrei-Florian Stoica ORCID iD [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Repository: CRAN
Date/Publication: 2025-09-18 08:50:07 UTC

Find the coordinates where a vertical or horizontal line intersects the hull

Description

This function finds the coordinates where a vertical or horizontal line intersects the hull.

Usage

borderCoords(df, axis, axisIntersect)

Arguments

df

A four-column data frame representing segments.

axis

An integer representing the axis intersected by the vertical or horizontal line, x (1) or y (2).

axisIntersect

The coordinate where the vertical or horizontal line intersects the relevant axis.

Value

A vector of size two representing the coordinates of the two intersection points between the vertical or horizontal line and the convex hull on the axis different from the input axis.

Add a centered title to a plot

Description

This function adds a centered title to a ggplot object.

Usage

centerTitle(p, title, ...)

Arguments

p

A ggplot object.

title

Plot title.

...

Other arguments passed to ggplot2::element_text.

Value

A ggplot object.

Store the radii of the circles and the corresponding number of edges

Description

This function stores the radii of the circles and the corresponding number of edges.

Usage

circleCoords(itemCoordsDF, extraCircles = 0)

Arguments

itemCoordsDF

Dataframe wih item coordinates

extraCircles

Number of circles drawn beyond those required to include the points representing the genes.

Value

A data frame containing the radius and the number of edges for each circle.

Plot item bars grouped by class

Description

This function plots bars for each item while grouping them by class and ordering them.

Usage

classPlot(
  df,
  title = "Class plot",
  xLab = "Value",
  yLab = "Item",
  legendLab = "Class",
  palette = "Spectral",
  labelSize = 2.5,
  labelColor = "black",
  decreasing = TRUE,
  valueCutoff = 0,
  ...
)

Arguments

df

A data frame with at least three columns, with class, item and value as the first three columns. The latter must be numeric.

title

Plot title.

xLab

Label of x axis.

yLab

Label of y axis.

legendLab

Legend label.

palette

grDevices palette.

labelSize

Label size. Ignored if labelDF is NULL.

labelColor

Label color.

decreasing

Whether to display the bars in decreasing order of length.

valueCutoff

Cutoff used for filtering the input data frame based on the value column. Only values greater than this cutoff will be displayed on the plot.

...

Other arguments passed to centerTitle.

Value

An object of class gg.

Examples

 df <- data.frame(Class = sample(paste0('C', seq(13)), 25, replace=TRUE),
 Item = paste0('I', seq(25)),
 Value = runif(25, 0.5, 1))
 classPlot(df)

 df <- data.frame(Class = sample(paste0('C', seq(13)), 25, replace=TRUE),
 Item = sample(paste0('I', seq(21)), 25, replace=TRUE),
 Value = runif(25, 0.5, 1))
 classPlot(df)

Find the connected components of a graph data frame

Description

This function finds the connected components of a graph data frame.

Usage

connectedComponents(df, colName = "component")

Arguments

df

A data frame with two categorical columns representing the edges of a graph.

colName

Name of the connected components column to be added.

Value

A data frame with a column indicating the connected component of each edge.

Examples

df <- data.frame(
gene1 = paste0('G', c(1, 2, 6, 7, 8, 9,
11, 25, 32, 17, 18)),
gene2 = paste0('G', c(2, 8, 8, 8, 1, 25,
32, 24, 24, 26, 26))
)
connectedComponents(df)

Construct the convex hull of a set of points

Description

This function constructs the convex hull of a set of points.

Usage

convexHull(pointsDF, hullIndices = NULL)

Arguments

pointsDF

A data frame with the x and y coordinates of the points.

hullIndices

Precalculated hull indices. Default is NULL: hull indices are not provided, but they are calculated by convexHull.

Details

The points must be provided as a data frame with two columns.

Value

A data frame with two columns representing the points on the convex hull.

Examples

pointsDF <- data.frame(a = c(1, 2, 2, 3, 3, 4, 5, 6, 8, 6,
7, 8, 6, 8, 10, 3, 1),
b = c(2, 3, 4, 8, 5, 6, 5, 4, 8, 11, 13, 14, 2, 1, 2, 14, 9))
hull <- convexHull(pointsDF)

Plot a correlation matrix

Description

This function plots a correlation matrix.

Usage

correlationPlot(
  mat,
  title = "Correlation plot",
  legendLab = "Correlation",
  ...
)

Arguments

mat

A numeric matrix or data frame.

title

Plot title.

legendLab

Legend label.

...

Additional parameters passed to tilePlot.

Details

A thin wrapper around tilePlot.

Value

An object of class gg.

Examples

mat <- matrix(runif(100, -1, 1), nrow=10)
colnames(mat) <- paste0('I', seq(10))
mat <- round(cor(mat), 2)
correlationPlot(mat)

Create density plot

Description

This function creates a density plot.

Usage

densityPlot(
  df,
  title = "Density plot",
  colorScheme = c("sea", "lava", "custom"),
  useSchemeDefaults = FALSE,
  drawNN = TRUE,
  drawScores = FALSE,
  palette = NULL,
  segColor = "plum1",
  pointSize = 0.8,
  pointColor = "red",
  segType = c("dashed", "solid", "dotted", "dotdash", "longdash", "twodash"),
  segWidth = 0.4,
  legendPos = c("right", "none"),
  nGridPoints = 300,
  expandPerc = 20,
  labelSize = 2.5,
  labelColor = "black",
  labelRepulsion = 1,
  labelPull = 1,
  maxOverlaps = Inf,
  verbose = FALSE,
  ...
)

Arguments

df

A data frame with at least two columns, representing the x and y coordinates of the points. A score column can also be provided as the third column. Nearest neighbor information can be provided in the last column as a character vector with elements selected from the rownames.

title

Plot title.

colorScheme

Color scheme.

useSchemeDefaults

Whether to use the default segColor, pointColor and labelColor for scheme. Ignored if colorScheme is set to 'custom'.

drawNN

Whether to draw segments linking each point to its nearest neighbor.

drawScores

Whether to render scores on the plot. If set to TRUE, the third column of the input data frame will be numeric and scores will be taken from there.

palette

Color palette. Used only if color scheme is set to 'custom'.

segColor

Nearest neighbor segment color. Ignored if drawNN is set to FALSE, or if useSchemeDefaults is TRUE and colorScheme is different from 'custom'.

pointSize

Point size.

pointColor

Point color. Ignored if useSchemeDefaults is TRUE and colorScheme is different from 'custom'.

segType

Nearest neighbor segment type. Must choose between 'solid', 'dashed', 'dotted','dotdash', 'longdash' and 'twodash'. Ignored if drawNN is set to FALSE.

segWidth

Nearest neighbor segment width. Ignored if drawNN is set to FALSE.

legendPos

Legend position. Choose between 'right' and 'none'.

nGridPoints

Number of grid points in each direction.

expandPerc

Percentage by which the grid will be expanded.

labelSize

Size of labels of strata elements.

labelColor

Label color. Ignored if useSchemeDefaults is TRUE and colorScheme is different from 'custom'.

labelRepulsion

Repulsion strength between labels.

labelPull

Attraction strength between a text label and its data point.

maxOverlaps

Maximum overlaps.

verbose

Whether output should be verbose.

...

Other arguments passed to centerTitle.

Value

An object of class gg.

Examples

x <- c(1, 2, 3, 4, 6, 7, 8, 10, 12, 11, 3, 6, 4, 1, 13, 13, 14, 18, 16)
y <- c(1, 3, 1, 4, 3, 2, 8, 2, 1, 11, 8, 8, 10, 14, 13, 11, 11, 12,15)
z <- round(runif(19, 75, 100), 2)
df <- data.frame(x, y, z)
rownames(df) <- paste0('p', rownames(df))
densityPlot(df)

Find the Euclidean distance between two points in a data frame

Description

This function finds the Euclidean distance between two points in a data frame.

Usage

dfEuclidean(df, i, j, pointCoords = c(1, 2), replaceZero = 0)

Arguments

df

A data frame containing the coordinates of the points.

i

Row name or index.

j

Row name or index

pointCoords

The row names or indices of point coordinates.

replaceZero

Value to replace zero with. If set to 0, no replacement will occur.

Value

A numeric value.

Extract point from data frame of points.

Description

This function extracts a point from a data frame of points.

Usage

dfPoint(df, i, pointCoords = c(1, 2))

Arguments

df

A data frame containing the coordinates of the points.

i

Row name or index.

pointCoords

The row names or indices of point coordinates.

Value

A numeric vector containing the point coordinates.

Map degrees to distances from the center and find the frequency of these distances

Description

This function interprets degrees as distances from a center (high degrees = low distances) and calculates the frequencies of these distances. Used later to draw concentric circles with the frequencies representing the number of points on a circle of the same radius.

Usage

distFreq(degreesDF)

Arguments

degreesDF

A data frame with names on the first column and positive integers on the second column.

Value

A data frame of distance frequencies.

Create a palette designed for densityPlot

Description

This function returns a palette designed for densityPlot.

Usage

dpColors(palette = c("sea", "lava"))

Arguments

palette

One of 'sea' and 'lava'.

Value

A character vector of colors.

Create the default hullPlot palette

Description

This function returns the default palette used by hullPlot.

Usage

hpColors()

Value

A character vector of colors.

Plot the convex hull of a set of points

Description

This function plots the convex hull of a set of points. It can also draw a vertical or a horizontal line (or both), dividing the hull into areas of different colors.

Usage

hullPlot(
  pointsDF,
  title = "Hull plot",
  xInt = NULL,
  yInt = NULL,
  borderColor = NULL,
  palette = hpColors(),
  hullWidth = 0,
  xLab = "x",
  yLab = "y",
  legendLabs = paste0("Group ", seq(4)),
  legendPos = "bottom",
  pointShape = 4,
  alpha = 0.2,
  labelDF = NULL,
  labelSize = 2.5,
  labelColor = "black",
  labelRepulsion = 1,
  labelPull = 0,
  maxOverlaps = 10,
  ...
)

Arguments

pointsDF

A data frame with the x and y coordinates of the points.

title

Plot title.

xInt

The coordinate where the vertical line intersects the x axis.

yInt

The coordinate where the horizontal line intersects the y axis.

borderColor

The color of the horizontal and vertical dividing lines, if provided. If NULL, no dividing lines will be drawn, though the hull will still be split along these lines (if xInt and/or yIntare not NULL).

palette

Color palette.

hullWidth

Width of the convex hull. If 0 (as default), the convex hull will not be displayed.

xLab

Label of x axis.

yLab

Label of y axis.

legendLabs

Legend labels.

legendPos

Legend position.

pointShape

Point shape.

alpha

Opaqueness level for the colors of the alluvia.

labelDF

Label data frame.

labelSize

Label size. Ignored if labelDF is NULL.

labelColor

Label color. Ignored if labelDF is NULL.

labelRepulsion

Repulsion strength between labels.

labelPull

Attraction strength between a text label and its data point.

maxOverlaps

Maximum overlaps. Ignored if labelDF is NULL.

...

Other arguments passed to centerTitle.

Value

An object of class gg.

Examples

pointsDF <- data.frame(x = c(1, 2, 4, 7, 10,
12, 13, 15, 16),
y = c(1, 1, 2, 3, 3, 2,
1, 2, 1))
hullPlot(pointsDF, 'Hull plot', 7, 1.5)

Check if a point is on a polygon boundary

Description

This function checks if a point P is on a polygon boundary.

Usage

isPointOnBoundary(xPoint, yPoint, boundary)

Arguments

xPoint

x coordinate of point P.

yPoint

y coordinate of point P.

boundary

A data frame with four columns representing segments comprising the boundary.

Value

Logical; whether the point is on the boundary.

Examples

pointsDF <- data.frame(x = c(1, 2, 4, 7, 10,
12, 13, 15, 16),
y = c(1, 1, 2, 3, 3, 2,
1, 2, 1))

hullIndices <- grDevices::chull(pointsDF[, 1], pointsDF[, 2])
hull <- convexHull(pointsDF, hullIndices)
hullSegments <- pointsToSegments(hull)

isPointOnBoundary(2, 3, hullSegments)

Check if a point is on a segment

Description

This function checks if a point P is on a segment AB.

Usage

isPointOnSeg(xPoint, yPoint, xStart, yStart, xEnd, yEnd)

Arguments

xPoint

x coordinate of point P.

yPoint

y coordinate of point P.

xStart

x coordinate of point A.

yStart

y coordinate of point A.

xEnd

x coordinate of point B.

yEnd

y coordinate of point B.

Value

Logical; whether the point is on the segment.

Examples

isPointOnSeg(2, 3, 1, 2, 3, 4)
isPointOnSeg(2, 3, 1, 2, 3, 8)
isPointOnSeg(4, 5, 1, 2, 3, 4)

Label points in a ggplot object

Description

This function labels points in a ggplot object.

Usage

labelPoints(
  p,
  labelDF,
  labelSize = 2,
  labelColor = "black",
  labelRepulsion = 1,
  labelPull = 1,
  maxOverlaps = Inf
)

Arguments

p

A ggplot object.

labelDF

Label data frame.

labelSize

Label size.

labelColor

Label color.

labelRepulsion

Repulsion strength between labels.

labelPull

Attraction strength between a text label and its data point.

maxOverlaps

Maximum overlaps.

Value

A ggplot object.

Plot graph with different colors for connected components

Description

This function plots the graph of the data frame, using different colors for nodes belonging to different connected components.

Usage

networkPlot(
  df,
  title = "Network plot",
  rankCol = "rank",
  edgeScale = 2,
  nodePointSize = 10,
  nodeTextSize = 2.3,
  palette = "Pastel 1",
  ...
)

Arguments

df

Data frame.

title

Plot title.

rankCol

Name of the rank column.

edgeScale

Scaling factor used in generating edge weights.

nodePointSize

Point size of graph nodes.

nodeTextSize

Text size of graph nodes.

palette

grDevices palette.

...

Other arguments passed to centerTitle.

Value

An object of class ggraph.

Examples

df <- data.frame(gene1 = paste0('G', c(1, 2, 5, 6, 7, 17)),
gene2 = paste0('G', c(2, 5, 8, 11, 11, 11)),
rank = c(1, 1, 3, 3, 3, 3))
networkPlot(df)

Prepare data frame for network plot

Description

This function prepares a data frame for network plot.

Usage

networkPlotDF(df, rankCol = "rank", edgeScale = 2)

Arguments

df

Data frame.

rankCol

Name of the rank column.

edgeScale

Scaling factor used in generating edge weights.

Value

A data frame ready to serve as input to networkPlot.

Construct a data frame of segments from a data frame of points

Description

This function constructs a data frame of segments from a data frame of points.

Usage

pointsToSegments(pointsDF, joinEnds = TRUE)

Arguments

pointsDF

A data frame with the x and y coordinates of the points. Each point must appear only once.

joinEnds

Whether to join the last point with the first one.

Value

A data frame of segments represented using four columns (x, y, xEnd, yEnd).

Examples

pointsDF <- data.frame(x = c(1, 2, 4, 7, 10,
12, 13, 15, 16),
y = c(1, 1, 2, 3, 3, 2, 1, 2, 1))

hullIndices <- grDevices::chull(pointsDF[, 1], pointsDF[, 2])
hull <- convexHull(pointsDF, hullIndices)
pointsToSegments(hull)

Find the coordinates of the points establishing the four divisions of the hull

Description

This function finds the coordinates of the points establishing the four divisions of the hull

Usage

quadBorders(pointsDF, xInt, yInt, vCoords, hCoords)

Arguments

pointsDF

A data frame with the x and y coordinates of the points.

xInt

The coordinate where the vertical line intersects the x axis.

yInt

The coordinate where the horizontal line intersects the y axis.

vCoords

The y coordinates of the two points where the vertical line intersects the convex hull.

hCoords

The x coordinates of the two points where the horizontal line intersects the convex hull.

Value

A data frame with 2 columns representing the 12 points (not unique) determining the boundaries of the hull divisions.

Draw radial plot for a degrees data frame

Description

This function draws a radial plot for a degrees data frame, plotting positive integer-valued points over concentric circles, with points located more centrally representing higher values.

Usage

radialPlot(
  degreesDF,
  title = "Radial plot",
  degreeLegendTitle = "Degree",
  groupLegendTitle = "Group",
  extraCircles = 0,
  palette = rpColors(length(unique(degreesDF[, 3]))),
  labelSize = 3,
  pointSize = 0.8,
  labelRepulsion = 1,
  labelPull = 0,
  maxOverlaps = 10,
  ...
)

Arguments

degreesDF

A data frame with names on the first column and positive integers on the second column.

title

Plot title.

degreeLegendTitle

Legend title corresponding to the positive integer column.

groupLegendTitle

Legend title corresponding to the categorical column.

extraCircles

Number of circles drawn beyond those required to include the points representing the genes.

palette

Color palette.

labelSize

Label size.

pointSize

Point size.

labelRepulsion

Repulsion strength between labels.

labelPull

Attraction strength between a text label and its data point.

maxOverlaps

Maximum overlaps. Ignored if labelDF is NULL.

...

Other arguments passed to centerTitle.

Value

An object of class gg.

Examples

degreesDF <- data.frame(Protein = paste0('P', seq(20)),
Degree = sample(10, 20, replace=TRUE),
Group = sample(3, 20, replace=TRUE))
radialPlot(degreesDF)

Create a rank plot

Description

This function creates a rank plot.

Usage

rankPlot(
  df,
  title = "Rank plot",
  summarize = TRUE,
  viridisPal = "turbo",
  xLab = "Item",
  yLab = "Rank count",
  legendLab = "Rank",
  sigDigits = NULL,
  labelSize = 2.5,
  labelColor = "black",
  labelFace = c("plain", "bold", "italic", "bold-italic"),
  xAngle = 45,
  vJust = 0.6,
  ...
)

Arguments

df

A data frame with ranks as columns and items as rows, or a summary data frame generated with rankSummary. If the latter, summarize must be set to FALSE.

title

Plot title.

summarize

Whether to summarize the ranks with rankSummary. Must be set to FALSE if the input data frame has been generated with rankSummary.

viridisPal

Viridis palette.

xLab

Label of x axis.

yLab

Label of y axis.

legendLab

Legend label.

sigDigits

Number of significant digits used when displaying mean ranks. If NULL, the mean ranks will not be displayed.

labelSize

Size of label marking average rank for each item. Ignored if showMeanRanks is FALSE.

labelColor

Color of label marking average rank for each item. Ignored if showMeanRanks is FALSE.

labelFace

Font face of label marking average rank for each item. Must be one among 'plain', 'bold', 'italic' and 'bold-italic'. Ignored if showMeanRanks is FALSE.

xAngle

Angle of x axis text.

vJust

Vertical justification in [0, 1].

...

Other arguments passed to centerTitle.

Value

An object of class gg.

Examples

df <- do.call(cbind, lapply(seq(30), function(i) sample(10, 10)))
rownames(df) <- paste0('M', seq(10))
colnames(df) <- paste0('R', seq(30))
rankPlot(df)

Create a rank summary

Description

This function creates a summary of multiple ranks provided for input items.

Usage

rankSummary(df)

Arguments

df

A data frame with ranks as columns, items as rows.

Value

A rank summary data frame with three columns: 'Rank', 'Item' and 'Count'.

Examples

df <- do.call(cbind, lapply(seq(30), function(i) sample(10, 10)))
rownames(df) <- paste0('M', seq(10))
colnames(df) <- paste0('R', seq(30))
rankSummary(df)

Create an alluvial plot

Description

This function creates an alluvial plot.

Usage

riverPlot(
  df,
  title = "River plot",
  fillColIndex = 2,
  curveType = "sigmoid",
  alpha = 0.8,
  strataFill = "lightgoldenrod1",
  labelSize = 3,
  viridisPal = "turbo",
  legendPos = "none",
  margins = margin(0, -10, -10, -10),
  ...
)

Arguments

df

A data frame with two categorical columns and a numeric column.

title

Plot title.

fillColIndex

Index of column used for coloring the alluvia.

curveType

Curve type.

alpha

Opaqueness level for the colors of the alluvia.

strataFill

Color used for the strata.

labelSize

Size of labels of strata elements.

viridisPal

Viridis palette.

legendPos

Legend position.

margins

Plot margins. Must be a vector of size 4 listing the desired top, right, bottom and left margin, in that order.

...

Other arguments passed to centerTitle.

Value

An object of class gg.

Examples

df <- data.frame(x = sample(c('a','b', 'c', 'd', 'e', 'f'), 20,
replace=TRUE),
y = sample(c('p','q', 'r', 's', 't', 'u', 'v', 'w'), 20,
replace=TRUE),
z = runif(20, 1, 3))
riverPlot(df)

Create a palette designed to represent dots over a viridis background

Description

This function returns a 10-color palette used as the default of radialPlot.

Usage

rpColors(nColors = 10)

Arguments

nColors

Number of colors.

Value

A character vector of colors.

Split the convex hull in four parts along two input lines

Description

This function splits the convex hull in two parts along a vertical and a horizontal line.

Usage

splitHull(
  p,
  pointsDF,
  hullSegments,
  xInt = NULL,
  yInt = NULL,
  borderColor = NULL,
  legendLabs = paste0("Group ", seq(4)),
  alpha = 0.5
)

Arguments

p

A ggplot object representing the hull.

pointsDF

A data frame with the x and y coordinates of the points.

hullSegments

Data frame of segments that define the convex hull.

xInt

The coordinate where the vertical line intersects the x axis.

yInt

The coordinate where the horizontal line intersects the y axis.

borderColor

The color of the horizontal and vertical dividing lines, if provided. If NULL, no dividing lines will be drawn, though the hull will still be split along these lines (if xInt and/or yIntare not NULL).

legendLabs

Legend labels.

alpha

Opaqueness level.

Value

An object of class gg showing the hull split along the input axes.

Split the convex hull in two along an input line

Description

This function splits the convex hull in two along an input vertical or horizontal line.

Usage

splitInTwo(
  p,
  pointsDF,
  axisIntersect,
  pointCoords,
  borderPoints,
  legendLabs = paste0("Group ", seq(2)),
  alpha = 0.5
)

Arguments

p

A ggplot object representing the hull.

pointsDF

A data frame with the x and y coordinates of the points.

axisIntersect

The coordinate where the vertical or horizontal line intersects the relevant axis.

pointCoords

The coordinates of the input points on the axis perpendicular to the input border line.

borderPoints

The points where the border line intersects the convex hull.

legendLabs

Legend labels.

alpha

Opaqueness level.

Value

A ggplot object showing the hull split in two parts along the input line.

Plot a numeric matrix or data frame

Description

This function plots a numeric matrix or data frame.

Usage

tilePlot(
  mat,
  title = "Tile plot",
  xLab = "x",
  yLab = "y",
  legendLab = "Value",
  sigDigits = 2,
  isCor = FALSE,
  labelSize = 3,
  labelColor = "black",
  tileBoundaryColor = "white",
  tileBoundaryWidth = 0.2,
  palette = "Spectral",
  reverseColors = TRUE,
  xAngle = 45,
  vJust = 0.6,
  ...
)

Arguments

mat

A numeric matrix or data frame.

title

Plot title.

xLab

Label of x axis.

yLab

Label of y axis.

legendLab

Legend label.

sigDigits

Number of significant digits to be displayed for each matrix element.

isCor

Whether the matrix is a correlation matrix, in which case the limits of the color scale will be set to [-1, 1].

labelSize

Label size. Ignored if labelDF is NULL.

labelColor

Label color.

tileBoundaryColor

Tile boundary color.

tileBoundaryWidth

Tile boundary width.

palette

grDevices palette.

reverseColors

Whether to reverse the order of colors in the palette.

xAngle

Angle of x axis text.

vJust

Vertical justification in [0, 1].

...

Other arguments passed to centerTitle.

Value

An object of class gg.

Examples

mat <- matrix(round(runif(100, 0, 1), 2), nrow=10)
rownames(mat) <- paste0('R', seq(10))
colnames(mat) <- paste0('C', seq(10))
tilePlot(mat)

Return the connected components of vertices

Description

This function returns the connected components of vertices from a graph data frame in which edges have been assigned connected components.

Usage

vertexComponents(df, colName = "component")

Arguments

df

A data frame with two categorical columns representing graph edges and a connected components column.

colName

Name of the connected components column.

Value

A factor vector representing the connected component of each vertex.

Examples

df <- data.frame(gene1 = c('A', 'B', 'C', 'A'),
gene2 = c('B', 'D', 'F', 'G'),
component = c(1, 1, 2, 1))
vertexComponents(df)