Help for package henna

Type:

Package

Title:

A Versatile Visualization Suite

Version:

0.7.5

Description:

A visualization suite primarily designed for single-cell RNA-sequencing data analysis applications but well-suited for 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, alluvial and volcano plots) for ease of usage and flexibility.

License:

MIT + file LICENSE

Imports:

abdiv, dplyr, ggalluvial, ggeasy, ggforce, ggraph, ggnewscale, ggplot2, ggrepel, grDevices, liver, methods, paletteer, reshape2, rlang, stats, tidygraph, viridis, withr

Encoding:

UTF-8

RoxygenNote:

7.3.3

Suggests:

EnhancedVolcano, qs2, testthat (≥ 3.0.0)

URL:

https://github.com/andrei-stoica26/henna

BugReports:

https://github.com/andrei-stoica26/henna/issues

Config/testthat/edition:

NeedsCompilation:

Packaged:

2026-02-17 07:32:32 UTC; Andrei

Author:

Andrei-Florian Stoica

[aut, cre]

Maintainer:

Andrei-Florian Stoica <andreistoica@foxmail.com>

Repository:

CRAN

Date/Publication:

2026-02-17 07:50:02 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 values

Description

This function stores the radii of the circles and the corresponding value for each circle.

Usage

circleCoords(itemCoordsDF, extraCircles = 0)

Arguments

itemCoordsDF

Data frame wih item coordinates.

extraCircles

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

Value

A data frame containing the radius and the corresponding value for each circle.

Plot bars for item counts grouped and colored by class

Description

This function plots bars for item counts grouped and colored by class.

Usage

classPlot(
  df,
  title = NULL,
  xLab = "Value",
  yLab = "Item",
  legendTitle = "Class",
  palette = "Spectral",
  labelSize = 2.5,
  labelColor = "black",
  legendTitleSize = 10,
  legendTextSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  decreasing = TRUE,
  valueCutoff = 0,
  ...
)

Arguments

df

A data frame with at least three columns. Its first column (categorical) colors the plot bars. The second column (categorical) labels the plots bars. The third column (numeric) sets the bar lengths.

title

Plot title.

xLab

x axis label.

yLab

y axis label.

legendTitle

Legend title.

palette

Color palette.

labelSize

Label size.

labelColor

Label color.

legendTitleSize

Legend title size.

legendTextSize

Legend text size.

axisTextSize

Axis text size.

axisTitleSize

Axis title size.

decreasing

Whether to display the bars in decreasing order of length.

valueCutoff

Cutoff used for filtering the input data frame based on the third (value) column. Only values above this cutoff will be displayed on the plot.

...

Additional 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 represented as a data frame

Description

This function finds the connected components of a graph represented as a 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 = NULL, legendTitle = "Correlation", ...)

Arguments

mat

A numeric matrix or data frame.

title

Plot title.

legendTitle

Legend title.

...

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 a label data frame

Description

This function creates a label data frame to be used by plotting functions that label selected points.

Usage

createLabelDFTemplate(
  df,
  xCol = 1,
  yCol = 2,
  labeledPoints = NULL,
  labelOutside = FALSE,
  labXThr = NULL,
  labYThr = NULL,
  adjFunX = identity,
  adjFunY = identity,
  compFunX = `>=`,
  compFunY = `>=`
)

Arguments

df

A data frame.

xCol

Column representing the x axis.

yCol

Column representing the y axis.

labeledPoints

Point labels to be displayed on the plot. Default is NULL, entailing that point labels will be displayed on the basis of labXThr and labYThr, if at least one of them is not NULL.

labelOutside

Display labels for points specified by labeledPoints even if they fall outside the boundaries imposed by labXThr and labYThr. Ignored if labeledPoints is NULL or both labXThr and labYThr are NULL.

labXThr

Threshold used to plot labels based on xCol values.

labYThr

Threshold used to plot labels based on yCol values.

adjFunX

Function used to adjust xCol values. Default is identity (no adjustment will be performed).

adjFunY

Function used to adjust yCol values. Default is identity (no adjustment will be performed).

compFunX

Function used for the selection of xCol values based on labXThr.

compFunY

Function used for the selection of yCol values based on labYThr.

Value

A label data frame.

Create density plot

Description

This function creates a density plot.

Usage

densityPlot(
  df,
  title = NULL,
  colorScheme = c("cloudy", "cake", "grapes", "lava", "oasis", "orichalc", "sea", "sky",
    "custom"),
  useSchemeDefaults = TRUE,
  drawNN = TRUE,
  drawScores = FALSE,
  xLab = NULL,
  yLab = NULL,
  legendTitle = "Density",
  palette = NULL,
  segColor = "black",
  pointSize = 1,
  pointColor = "red",
  segType = c("dashed", "solid", "dotted", "dotdash", "longdash", "twodash"),
  segWidth = 0.4,
  nGridPoints = 300,
  expandPerc = 20,
  labelType = c("free", "boxed"),
  labelSize = 3,
  labelColor = "black",
  labelRepulsion = 1,
  labelPull = 1,
  maxOverlaps = 10,
  labelPadding = 0,
  boxPadding = 0,
  labelSegWidth = 0.4,
  legendPos = c("right", "none"),
  legendTextSize = 10,
  legendTitleSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  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. Choose between 'cake', 'cloudy', 'grapes', 'lava', oasis', 'orichalc', 'sea', 'sky' and 'custom'. Default is 'cloudy'.

useSchemeDefaults

Whether to use the default segColor, pointColor and labelColor values 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.

xLab

x axis label.

yLab

y axis label.

legendTitle

Legend title.

palette

A character vector of colors. 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. 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.

nGridPoints

Number of grid points in each direction.

expandPerc

Percentage by which the grid will be expanded.

labelType

Whether to draw a box around labels (option 'boxed') or not (option 'free'). Default is 'free'.

labelSize

Label size.

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 number of allowed overlaps.

labelPadding

Amount of padding around label.

boxPadding

Amount of padding around box.

labelSegWidth

Thickness of segment connecting label to point.

legendPos

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

legendTextSize

Legend text size.

legendTitleSize

Legend title size.

axisTextSize

Axis text size.

axisTitleSize

Axis title size.

verbose

Whether output should be verbose.

...

Additional 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 values to distances from the center and find the frequency of these distances

Description

This function interprets values as distances from a center (high values = low distances) and calculates the frequencies of these distances.

Usage

distFreq(valuesDF)

Arguments

valuesDF

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

Details

Used later to draw concentric circles with the frequencies representing the number of points on a circle of the same radius.

Value

A data frame of distance frequencies.

Internal function used for documenting other functions

Description

This function is used internally to help document other functions.

Usage

documentFun(
  title = NULL,
  xLab = "x",
  yLab = "y",
  legendTitle = "Legend",
  legendLabs = c("a", "b"),
  legendPos = "right",
  palette = "Spectral",
  viridisPal = "turbo",
  labeledPoints = NULL,
  labelType = "free",
  labelOutside = TRUE,
  labelSize = 2.5,
  labelColor = "black",
  labelRepulsion = 1,
  labelPull = 1,
  maxOverlaps = 50,
  boxPadding = 0.2,
  labelPadding = 0.1,
  labelSegWidth = 0.4,
  pointSize = 0.8,
  pointShape = 1,
  legendTitleSize = 10,
  legendTextSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  xAngle = 45,
  vJust = 0.6,
  margins = margin(0, -10, -10, -10),
  theme = "linedraw",
  pvalOffset = 1.00000023069254e-317,
  ...
)

Arguments

title

Plot title.

xLab

x axis label.

yLab

y axis label.

legendTitle

Legend title.

legendLabs

Legend labels.

legendPos

Legend position.

palette

Color palette.

viridisPal

Viridis palette.

labeledPoints

Point labels to be displayed on the plot.

labelType

Whether to draw a box around labels (option 'boxed') or not (option 'free'). Default is 'free'.

labelSize

Label size.

labelColor

Label color.

labelRepulsion

Repulsion strength between labels.

labelPull

Attraction strength between a text label and its data point.

maxOverlaps

Maximum number of allowed overlaps.

boxPadding

Amount of padding around box.

labelPadding

Amount of padding around label.

labelSegWidth

Thickness of segment connecting label to point.

pointSize

Point size.

pointShape

Point shape.

legendTitleSize

Legend title size.

legendTextSize

Legend text size.

axisTextSize

Axis text size.

axisTitleSize

Axis title size.

xAngle

Angle of x axis text.

vJust

Vertical justification in [0, 1].

margins

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

theme

Plot theme.

pvalOffset

Offset added to p-values to avoid infinite values when taking logarithms.

...

Additional arguments passed to centerTitle.

Value

NULL. This function is only used internally for documentation.

Create a palette designed for densityPlot

Description

This function returns a palette designed for densityPlot.

Usage

dpColors(
  palette = c("cake", "cloudy", "grapes", "lava", "oasis", "orichalc", "sea", "sky")
)

Arguments

palette

One of 'lava', 'oasis', 'orichalc', 'sea' and 'sky'.

Value

A character vector of colors.

Examples

dpColors('sea')

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 = NULL,
  xInt = NULL,
  yInt = NULL,
  palette = hpColors(),
  lineColor = "navy",
  lineWidth = 0.3,
  lineType = c("dashed", "solid", "dotted", "dotdash", "longdash", "twodash"),
  hullWidth = 0,
  xLab = NULL,
  yLab = NULL,
  legendLabs = paste0("Group ", seq(4)),
  pointSize = 1,
  pointShape = 4,
  alpha = 0.2,
  labeledPoints = NULL,
  labelOutside = FALSE,
  labXThr = NULL,
  labYThr = NULL,
  labelType = c("free", "boxed"),
  labelSize = 2.5,
  labelColor = "black",
  labelRepulsion = 1,
  labelPull = 0,
  maxOverlaps = 10,
  legendPos = "bottom",
  legendTextSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  ...
)

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.

palette

Color palette.

lineColor

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.

lineWidth

The width of the horizontal and vertical dividing lines. Ignored if lineColor is NULL.

lineType

The type of the horizontal and vertical dividing lines. Choose between 'dashed','solid', 'dotted', 'dotdash', 'longdash' and 'twodash'. Default is 'dashed'. Ignored if lineColor is NULL.

hullWidth

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

xLab

x axis label.

yLab

y axis label.

legendLabs

Legend labels.

pointSize

Point size.

pointShape

Point shape.

alpha

Opaqueness level.

labeledPoints

Point labels to be displayed on the plot.

labelOutside

labXThr

Threshold used to plot labels based on xCol values.

labYThr

Threshold used to plot labels based on yCol values.

labelType

Whether to draw a box around labels (option 'boxed') or not (option 'free'). Default is 'free'.

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.

legendPos

Legend position.

legendTextSize

Legend text size.

axisTextSize

Axis text size.

axisTitleSize

Axis title size.

...

Additional 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,
  pointLabs = rownames(labelDF),
  labelType = c("free", "boxed"),
  labelSize = 2.5,
  labelColor = "black",
  labelRepulsion = 1,
  labelPull = 1,
  maxOverlaps = 50,
  boxPadding = 0.2,
  labelPadding = 0.1,
  labelSegWidth = 0.4,
  ...
)

Arguments

p

A ggplot object.

labelDF

Label data frame.

pointLabs

Labels of points.

labelType

Whether to draw a box around labels (option 'boxed') or not (option 'free'). Default is 'free'.

labelSize

Label size.

labelColor

Label color.

labelRepulsion

Repulsion strength between labels.

labelPull

Attraction strength between a text label and its data point.

maxOverlaps

Maximum number of allowed overlaps.

boxPadding

Amount of padding around box.

labelPadding

Amount of padding around label.

labelSegWidth

Thickness of segment connecting label to point.

...

Additional arguments passed to geom_text_repel (if labelType is 'free') or geom_text_label (if labelType is 'boxed').

Value

A ggplot object.

Examples

filePath <- system.file('extdata', 'hullPlot.qs2', package='henna')
sharedDF <- qs2::qs_read(filePath)
name1 <- 'alpha'
name2 <- 'delta'
legendLabs <- as.factor(c('Non-top',
'Shared',
paste0('Top only for ', name2),
paste0('Top only for ', name1)))
p <- hullPlot(sharedDF, 'Shared markers plot', xInt=1.5, yInt=1.3,
xLab=paste0('avg_log2FC (', name1, ')'),
yLab=paste0('avg_log2FC (', name2, ')'),
legendLabs=legendLabs)
labelDF <- sharedDF[sharedDF[, 'avg_log2FC_1'] > 1.5 &
sharedDF[, 'avg_log2FC_2'] > 1.3, ]
p <- labelPoints(p, labelDF, labelType='boxed', nudge_x=0.1, nudge_y=0.1)

Plot graph with the option of using different colors for connected components

Description

This function plots the graph of the data frame and optionally uses different colors for nodes belonging to different connected components.

Usage

networkPlot(
  df,
  title = NULL,
  numCol = NULL,
  numColType = c("weights", "ranks"),
  nodeSize = 10,
  nodeTextSize = 2.3,
  palette = "grDevices::Spectral",
  nodeColor = NULL,
  edgeWidth = 1,
  edgeColor = "black",
  edgeScales = c(0.2, 0.6),
  ...
)

Arguments

df

Data frame.

title

Plot title.

numCol

Name of the numeric column used to vary edge widths. If no such column is provided, set to NULL.

numColType

The type of the numeric column used to vary edge widths. Choose between 'weights' and 'ranks' Ignored if numCol is NULL.

nodeSize

Size of graph nodes.

nodeTextSize

Size of text on graph nodes.

palette

grDevices palette used for coloring nodes. Ignored if nodeColor is not NULL.

nodeColor

Color used for nodes. Default is NULL (palette will instead be used).

edgeWidth

Width to be used for all edges before scaling if numCol is NULL; otherwise ignored.

edgeColor

Color used for edges.

edgeScales

Edge width scales. Must be a numeric vector of size 2 (minimum and maximum).

...

Additional 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, numCol='rank', numColType='ranks')

Prepare data frame for network plot

Description

This function prepares a data frame for network plot.

Usage

networkPlotDF(df, rankCol = "rank")

Arguments

df

Data frame.

rankCol

Name of the rank column.

Value

A data frame ready to serve as input to networkPlot.

Generate the coordinates of points on a circle centered at origin

Description

This function generates nPoints on a circle of radius r centered at origin.

Usage

pointsOnCircle(r, nPoints, seed = 50)

Arguments

r

Radius.

nPoints

Number of points.

seed

Random seed.

Value

A data frame with the coordinates of the points.

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 data frame with positive integer-valued points

Description

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

Usage

radialPlot(
  valuesDF,
  title = NULL,
  valueLegendTitle = "Value",
  groupLegendTitle = NULL,
  extraCircles = 0,
  palette = rpColors(length(unique(valuesDF[, 3]))),
  labelSize = 3,
  pointSize = 0.8,
  legendTitleSize = 10,
  legendTextSize = 10,
  labelRepulsion = 1,
  labelPull = 0,
  maxOverlaps = 15,
  breakDensity = 6,
  seed = 50,
  ...
)

Arguments

valuesDF

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

title

Plot title.

valueLegendTitle

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.

palette

Color palette.

labelSize

Label size.

pointSize

Point size.

legendTitleSize

Legend title size.

legendTextSize

Legend text size.

labelRepulsion

Repulsion strength between labels.

labelPull

Attraction strength between a text label and its data point.

maxOverlaps

Maximum number of allowed overlaps.

breakDensity

Factor used in calculating the number of breaks for the values legend. Higher values of this argument add more breaks to the legend, but no breaks at a distance below 1 will be allowed.

seed

Random seed.

...

Additional arguments passed to centerTitle.

Value

An object of class gg.

Examples

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

Create a rank plot

Description

This function creates a rank plot.

Usage

rankPlot(
  df,
  title = NULL,
  summarize = TRUE,
  viridisPal = "turbo",
  xLab = "Item",
  yLab = "Rank count",
  legendTitle = "Rank",
  sigDigits = NULL,
  labelSize = 2.5,
  labelColor = "black",
  labelFace = c("plain", "bold", "italic", "bold-italic"),
  legendTextSize = 10,
  legendTitleSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  xAngle = 45,
  vJust = 0.6,
  labelScalingFactor = 0.9,
  labelOffset = 0.05,
  ...
)

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

y axis label.

legendTitle

Legend title.

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 sigDigits is NULL.

labelColor

Color of label marking average rank for each item. Ignored if sigDigits is NULL.

labelFace

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

legendTextSize

Legend text size.

legendTitleSize

Legend title size.

axisTextSize

Axis text size.

axisTitleSize

Axis title size.

xAngle

Angle of x axis text.

vJust

Vertical justification in [0, 1].

labelScalingFactor

Scaling factor used when displaying mean ranks. Ignored if sigDigits is NULL.

labelOffset

Vertical offset used when displaying mean ranks. Ignored if sigDigits is NULL.

...

Additional 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 and 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)

Sort a data frame by the first column and convert the second to a factor

Description

This function sort a data frame by the first column and convert the second to a factor.

Usage

reorderDF(df)

Arguments

df

A data frame.

Value

An object of class gg.

Examples

df <- data.frame(a = c(2, 4, 1, 3, 6),
b = c(2, 8, 3, 19, 3))
reorderDF(df)

Create an alluvial plot

Description

This function creates an alluvial plot.

Usage

riverPlot(
  df,
  title = NULL,
  fillColIndex = 2,
  curveType = "sigmoid",
  alpha = 0.8,
  strataFill = "lightgoldenrod1",
  labelSize = 3,
  axisTextSize = 12,
  axisTitleSize = 12,
  viridisPal = "turbo",
  ...
)

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.

axisTextSize

Axis text size.

axisTitleSize

Axis title size.

viridisPal

Viridis palette.

...

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,
  lineColor = "navy",
  lineWidth = 0.3,
  lineType = c("dashed", "solid", "dotted", "dotdash", "longdash", "twodash"),
  legendLabs = paste0("Group ", seq(4)),
  alpha = 0.2
)

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.

lineColor

lineWidth

The width of the horizontal and vertical dividing lines. Ignored if lineColor is NULL.

lineType

The type of the horizontal and vertical dividing lines. Choose between 'dashed','solid', 'dotted', 'dotdash', 'longdash' and 'twodash'. Default is 'dashed'. Ignored if lineColor is 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 = NULL,
  xLab = NULL,
  yLab = NULL,
  legendTitle = "Value",
  palette = "Spectral",
  reverseColors = TRUE,
  sigDigits = 2,
  isCor = FALSE,
  labelSize = 3,
  labelColor = "black",
  legendTextSize = 10,
  legendTitleSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  tileBoundaryColor = "white",
  tileBoundaryWidth = 0.2,
  xAngle = 45,
  vJust = 0.6,
  ...
)

Arguments

mat

A numeric matrix or data frame.

title

Plot title.

xLab

x axis label.

yLab

y axis label.

legendTitle

Legend title.

palette

Color palette.

reverseColors

Whether to reverse the order of colors in the palette.

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.

labelColor

Label color.

legendTextSize

Legend text size.

legendTitleSize

Legend title size.

axisTextSize

Axis text size.

axisTitleSize

Axis title size.

tileBoundaryColor

Tile boundary color.

tileBoundaryWidth

Tile boundary width.

xAngle

Angle of x axis text.

vJust

Vertical justification in [0, 1].

...

Additional 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)

Create a volcano plot

Description

This function creates a volcano plot for a data frame with a log column and a p-value column. The gene names must be provided as row names.

Usage

volcanoPlot(
  df,
  title = NULL,
  logCol = "avg_log2FC",
  pvalCol = "p_val_adj",
  xLab = expression(log[2] ~ fold ~ change),
  yLab = expression(-log[10] ~ `p-value`),
  legendTitle = "Significance",
  legendLabs = c("Not significant", expression(log[2] ~ FC), "p-value",
    expression(`p-value` ~ and ~ log[2] ~ FC)),
  legendPos = c("right", "top", "left", "bottom"),
  logFCThr = 1,
  pvalThr = 1e-05,
  labeledGenes = NULL,
  labelOutside = FALSE,
  labLogFCThr = 1.8,
  labPvalThr = 1e-12,
  labelType = c("boxed", "free"),
  labelSize = 2.2,
  labelColor = "black",
  labelRepulsion = 1,
  labelPull = 0,
  maxOverlaps = 100,
  boxPadding = 0.2,
  labelPadding = 0.1,
  labelSegWidth = 0.4,
  pointSize = 0.8,
  alpha = 0.6,
  palette = c("gray31", "goldenrod2", "orchid3", "red2"),
  legendTextSize = 10,
  legendTitleSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  theme = c("minimal", "bw", "classic", "linedraw"),
  ...
)

Arguments

df

A data frame with rownames as genes, a log column and a p-value column.

title

Plot title.

logCol

Log column.

pvalCol

P-value column.

xLab

x axis label.

yLab

y axis label.

legendTitle

Legend title.

legendLabs

Legend labels.

legendPos

Legend position.

logFCThr

Threshold used to separate significant log values.

pvalThr

Threshold used to separate significant p-values.

labeledGenes

Gene labels to be displayed on the plot. Default is NULL, entailing that gene labels will be displayed on the basis of labLogFCThr and labPvalThr, if at least one of them is not NULL.

labelOutside

Display labels for points specified by labeledGenes even if they fall outside the boundaries imposed by labLogFCThr and labPvalThr. Ignored if labeledGenes is NULL or both labLogFCThr and labPvalThr are NULL.

labLogFCThr

Threshold used to plot gene labels based on log values. Ignored if labeledGenes is not NULL.

labPvalThr

Threshold used to plot gene labels based on p-values. Ignored if labeledGenes is not NULL.

labelType

Whether to draw a box around labels (option 'boxed') or not (option 'free'). Default is 'free'.

labelSize

Label size.

labelColor

Label color.

labelRepulsion

Repulsion strength between labels.

labelPull

Attraction strength between a text label and its data point.

maxOverlaps

Maximum number of allowed overlaps.

boxPadding

Amount of padding around box.

labelPadding

Amount of padding around label.

labelSegWidth

Thickness of segment connecting label to point.

pointSize

Point size.

alpha

Opaqueness level of point color.

palette

Color palette.

legendTextSize

Legend text size.

legendTitleSize

Legend title size.

axisTextSize

Axis text size.

axisTitleSize

Axis title size.

theme

Plot theme. Choose between 'bw', 'classic', 'linedraw' and 'minimal'. Default is 'minimal'.

...

Additional arguments passed to EnhancedVolcano::EnhancedVolcano.

Details

Users can input labeled genes in two ways:

1) By using p-value and log fold-change thresholds (the default option).

2) By inputting a list of labels.

Value

An object of class gg.

Examples

if (requireNamespace("EnhancedVolcano", quietly=TRUE)){
filePath <- system.file('extdata', 'volcanoPlot.qs2', package='henna')
df <- qs2::qs_read(filePath)
p <- volcanoPlot(df, title='Volcano plot - beta cells', pvalThr=1e-10,
logFCThr=1,
labPvalThr=1e-150,
labLogFCThr=5.3)
}