Title: Using 'ggplot2' Feature to Write Readable R Code for Circular Visualization
Version: 0.9.1
Description: A wrapper for 'circlize'. All components are based on classes and objects. Users can use the addition symbol (+) to combine components for a circular visualization with 'ggplot2' style.The package is described in Zhang Z, Cao T, Huang Y and Xia Y (2025) <doi:10.3389/fgene.2025.1535368>.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
Collate: 'track.R' 'heatmap.R' 'cell-geom.R' 'track-geom.R' 'link.R' 'param.R' 'utils.R' 'initialize.R' 'add.R' 'circlizePlus-package.R' 'data.R'
Depends: circlize (≥ 0.4.16), R (≥ 4.4.0)
Imports: methods, stats
Suggests: png, ape, dendextend, ComplexHeatmap, testthat (≥ 3.0.0), knitr, rmarkdown
Config/testthat/edition: 3
URL: https://github.com/TianzeLab/circlizePlus, https://tianzelab.github.io/circlizePlus/, https://doi.org/10.3389/fgene.2025.1535368
BugReports: https://github.com/TianzeLab/circlizePlus/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-05-23 09:05:12 UTC; caotianze
Author: Tianze Cao ORCID iD [aut, cre], Zheyu Zhang [aut]
Maintainer: Tianze Cao <hnrcao@qq.com>
Repository: CRAN
Date/Publication: 2025-05-23 09:22:02 UTC

circlizePlus: Using 'ggplot2' Feature to Write Readable R Code for Circular Visualization

Description

A wrapper for 'circlize'. All components are based on classes and objects. Users can use the addition symbol (+) to combine components for a circular visualization with 'ggplot2' style.The package is described in Zhang Z, Cao T, Huang Y and Xia Y (2025) doi:10.3389/fgene.2025.1535368.

Author(s)

Maintainer: Tianze Cao hnrcao@qq.com (ORCID)

Authors:

See Also

Useful links:

Addition rules in circlizePlus

Description

ccPlot(contain n ccTracks)+ccTrack=ccPlot(contain n+1 ccTracks),n>=0
ccPlot(contain n ccLinks)+ccLink=ccPlot(contain n+1 ccLinks),n>=0
ccTrak(contain n ccTrakGeoms)+ccTrackGeom=ccTrack(contain n+1 ccTrackGeoms),n>=0
ccTrack(contain n ccCells)+ccCell=ccTrack(contain n+1 ccCells),n>=0
ccCell(contain n ccCellGeoms)+ccCellGeom=ccCell(contain n+1 ccCellGeoms),n>=0

Usage

## S4 method for signature 'ccPlot,ccPar'
e1 + e2

## S4 method for signature 'ccPlot,ccTrack'
e1 + e2

## S4 method for signature 'ccPlot,ccLink'
e1 + e2

## S4 method for signature 'ccTrack,ccTrackGeom'
e1 + e2

## S4 method for signature 'ccTrack,ccCells'
e1 + e2

## S4 method for signature 'ccTrack,ccCell'
e1 + e2

## S4 method for signature 'ccCell,ccCellGeom'
e1 + e2

## S4 method for signature 'ccCells,ccCellGeom'
e1 + e2

## S4 method for signature 'ccHeatmap,ccPar'
e1 + e2

## S4 method for signature 'ccHeatmap,ccTrack'
e1 + e2

## S4 method for signature 'ccHeatmap,ccLink'
e1 + e2

Arguments

e1

A object defined in circlizePlus

e2

A object defined in circlizePlus

Value

A object defined in circlizePlus

Examples

NULL

Draw an arrow

Description

Object ccCellGeom will call the function circlize::circos.arrow while drawing.

Usage

ccArrow(
  x1,
  x2,
  y,
  width,
  arrow.head.length = NULL,
  arrow.head.width = width * 2,
  arrow.position = c("end", "start"),
  tail = c("normal", "point"),
  border = "black",
  col = "#FFCCCC",
  lty = par("lty"),
  ...
)

Arguments

x1

Start position of the arrow on the x-axis.

x2

End position of the arrow on the x-axis. Note x2 should be larger than x1. The direction of arrows can be controlled by arrow.position argument.

y

Position of the arrow on the y-axis. Note this is the center of the arrow on y-axis.

width

Width of the arrow body.

arrow.head.length

Length of the arrow head. Note the value should be smaller than the length of the arrow itself (which is x2 - x1).

arrow.head.width

Width of the arrow head.

arrow.position

Where is the arrow head on the arrow. If you want to the arrow in the reversed direction, set this value to "start".

tail

The shape of the arrow tail (the opposite side of arrow head).

border

Border color of the arrow.

col

Filled color of the arrow.

lty

Line style of the arrow.

...

Pass to polygon.

Value

Object ccCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(sectors = letters[1:4], xlim = c(0, 10))
track <- ccTrack(ylim = c(0, 1))
cell <- ccCell(sector.index = "a") + ccArrow(x1 = 1, x2 = 9, y=0.5, width=0.5)
track <- track + cell
cc + track

Draw barplots

Description

Object ccCellGeom will call the function circlize::circos.barplot while drawing.

Usage

ccBarplot(
  value,
  pos,
  bar_width = 0.6,
  col = NA,
  border = "black",
  lwd = par("lwd"),
  lty = par("lty")
)

Arguments

value

A numeric vector or a matrix. If it is a matrix, columns correspond to the height of bars.

pos

Positions of the bars.

bar_width

Width of bars. It assumes the bars locating at x = 1, 2, ....

col

Filled color of bars.

border

Color for the border.

lwd

Line width.

lty

Line style.

Value

Object ccCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(sectors = letters[1:4], xlim = c(0, 10))
track <- ccTrack(ylim = c(0, 1))
cell <- ccCell(sector.index = "a") + ccBarplot(value = runif(10), pos = 1:10 - 0.5, col = 1:10)
track <- track + cell
cc + track

Draw boxplots

Description

Object ccCellGeom will call the function circlize::circos.boxplot while drawing.

Usage

ccBoxplot(
  value,
  pos,
  outline = TRUE,
  box_width = 0.6,
  col = NA,
  border = "black",
  lwd = par("lwd"),
  lty = par("lty"),
  cex = par("cex"),
  pch = 1,
  pt.col = par("col")
)

Arguments

value

A numeric vector, a matrix or a list. If it is a matrix, boxplots are made by columns (each column is a box).

pos

Positions of the boxes.

outline

Whether to draw outliers.

box_width

Width of boxes.

col

Filled color of boxes.

border

Color for the border as well as the quantile lines.

lwd

Line width.

lty

Line style

cex

Point size.

pch

Point type.

pt.col

Point color.

Value

Object ccCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(sectors = letters[1:4], xlim = c(0, 10))
track <- ccTrack(ylim = c(0, 1))
cell <- ccCell(sector.index = "a") + ccBoxplot(value = replicate(runif(10),
n = 10, simplify = FALSE), pos = 1:10 - 0.5, col = 1:10)
track <- track + cell
cc + track

Generate a cell container that belongs to a particular sector

Description

Generate a cell container that belongs to a particular sector

Usage

ccCell(sector.index = NULL)

Arguments

sector.index

character. It is the index that corresponds to the sector.

Value

Object ccCell

Examples

library(circlizePlus)
sectors <- c("a", "a", "a", "a", "b", "b", "b", "b", "c", "c", "c", "c", "d", "d", "d", "d")
x1 <- c(1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4)
y1 <- c(1, 2, 3, 4, 4, 3, 2, 1, 1, 1, 1, 1, 1, 2, 1, 2)
cc <- ccPlot(initMode = "initialize", sectors = sectors, x = x1)
track1 <- ccTrack(sectors = sectors, x = x1, y = y1)
cell_single <- ccCell(sector.index = letters[3]) + ccPoints(y = \(x, y){
  y
})
track1 <- track1 + cell_single
cc + track1

S4 class ccCell

Description

A cell container that belongs to a particular sector.

Slots

sector.index

character. It is the index that corresponds to the sector.

geoms

list. The elements in the list should all be of type ccCellGeom or ccGenomicCellGeom.

Examples

NULL

S4 class ccCellGeom

Description

Objectified representation of the R package circlize's plotting functions and corresponding parameters at the cell level.

Slots

func

character. The name of the plot function in the R package circlize.

params

list. When the function corresponding to the parameter param is called, it represents the argument of this function.

Examples

NULL

Generate a list of multiple object ccCell-class

Description

Generate a list of multiple object ccCell-class

Usage

ccCells(sector.indexes = list())

Arguments

sector.indexes

list. A list of indexs that corresponds to the sectors.

Value

Object ccCells

Examples

library(circlizePlus)
sectors <- c("a", "a", "a", "a", "b", "b", "b", "b", "c", "c", "c", "c", "d", "d", "d", "d")
x1 <- c(1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4)
y1 <- c(1, 2, 3, 4, 4, 3, 2, 1, 1, 1, 1, 1, 1, 2, 1, 2)
cc <- ccPlot(initMode = "initialize", sectors = sectors, x = x1)
cells <- ccCells(sector.indexes = letters[1:4])
cc_point <- ccPoints()
cells <- cells + cc_point + ccLines()
track1 <- ccTrack(sectors = sectors, x = x1, y = y1)
track1 <- track1 + cells
cc + track1

S4 class ccCells

Description

A list of multiple ccCell. Any ccCellGeom and ccCells are added together as if they were added to each ccCell contained in the ccCells.

Examples

NULL

Draw dendrogram plots in a track

Description

Object ccCellGeom will call the function circlize::circos.dendrogram while drawing.

Usage

ccDendrogram(
  dend,
  facing = c("outside", "inside"),
  max_height = NULL,
  use_x_attr = FALSE
)

Arguments

dend

A dendrogram object.

facing

Is the dendromgrams facing inside to the circle or outside?

max_height

Maximum height of the dendrogram. This is important if more than one dendrograms are drawn in one track and making them comparable. The height of a dendrogram can be obtained by attr(dend, "height").

use_x_attr

Whether use the x attribute to determine node positions in the dendrogram, used internally.

Value

Object ccCellGeom

Examples


library(ape)
suppressPackageStartupMessages(library(dendextend))
library(circlizePlus)
data(bird.orders)
hc <- as.hclust(bird.orders)
labels <- hc$labels
ct <- cutree(hc, 6)
n <- length(labels)
dend <- as.dendrogram(hc)
par1 <- ccPar(cell.padding = c(0, 0, 0, 0))
cc <- ccPlot(sectors = "a", xlim = c(0, n)) # only one sector
dend <- color_branches(dend, k = 6, col = 1:6)
dend_height <- attr(dend, "height")
t1 <- ccTrack(ylim = c(0, dend_height), bg.border = NA, track.height = 0.4)
cell1 <- ccCell(sector.index = "a") + ccDendrogram(dend = dend)
cc + par1 + (t1 + cell1)

Add genomic axes

Description

Object ccGenomicCellGeom will call the function circlize::circos.genomicAxis while drawing.

Usage

ccGenomicAxis(
  h = "top",
  major.at = NULL,
  labels = NULL,
  major.by = NULL,
  tickLabelsStartFromZero = TRUE,
  labels.cex = 0.4 * par("cex"),
  ...
)

Arguments

h

Position of the axes. "top" or "bottom".

major.at

Major breaks. If major.at is set, major.by is ignored.

labels

labels corresponding to major.at. If labels is set, major.at must be set.

major.by

Increment of major ticks. It is calculated automatically if the value is not set (about every 10 degrees there is a major tick).

tickLabelsStartFromZero

Whether axis tick labels start from 0? This will only affect the axis labels while not affect x-values in cells.

labels.cex

The font size for the axis tick labels.

...

Other arguments pass to circos.axis.

Value

Object ccGenomicCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(initMode = "initializeWithIdeogram",
chromosome.index = paste0("chr", 1:4), plotType = NULL)
track <- ccTrack(ylim = c(0, 1))
cell <- ccCell(sector.index = "chr1") + ccGenomicAxis()
e <- track + cell
cc + e

S4 class ccGenomicCellGeom

Description

It is a subclass of ccCellGeom. It only works if the plotted data is genomic data. Objectified representation of the R package circlize's plotting functions and corresponding parameters at the cell level.

Slots

func

character. The name of the plot function in the R package circlize.

params

list. When the function corresponding to the parameter param is called, it represents the argument of this function.

Examples

NULL

Create a track of density plot

Description

Object ccGenomicTrack will call the function circlize::circos.genomicDensity while drawing.

Usage

ccGenomicDensity(
  data,
  ylim.force = FALSE,
  window.size = NULL,
  overlap = TRUE,
  count_by = c("percent", "number"),
  col = ifelse(area, "grey", "black"),
  lwd = par("lwd"),
  lty = par("lty"),
  type = "l",
  area = TRUE,
  area.baseline = NULL,
  baseline = 0,
  border = NA,
  ...
)

Arguments

data

A bed-file-like data frame or a list of data frames. If the input is a list of data frames. there will be multiple density plot in one same track.

ylim.force

Whether to force upper bound of ylim to be 1. Ignored if count_by is set to number.

window.size

Pass to genomicDensity.

overlap

Pass to genomicDensity.

count_by

Pass to genomicDensity.

col

Colors. It should be length of one. If data is a list of data frames, the length of col can also be the length of the list. If multiple sets of genomic regions are visualized in one single track, you should set the colors with transparency to distinguish them.

lwd

Width of lines, the same setting as col argument.

lty

Style of lines, the same setting as col argument.

type

Type of lines, see circos.lines.

area

See circos.lines.

area.baseline

Deprecated, use baseline instead.

baseline

See circos.lines.

border

See circos.lines.

...

Pass to circos.trackPlotRegion.

Value

Object ccGenomicTrack

Examples


library(circlizePlus)
load(system.file(package = "circlize", "extdata", "DMR.RData"))
cc = ccPlot(initMode="initializeWithIdeogram", chromosome.index = paste0("chr", 1:22))
t2 = ccGenomicDensity(DMR_hyper, col = c("#FF000080"), track.height = 0.1)
t3 = ccGenomicDensity(DMR_hypo, col = c("#0000FF80"), track.height = 0.1)
cc + t2 + t3
circos.clear()

Define a heatmap track for genomic graph

Description

Object ccGenomicTrack will call the function circlize::circos.genomicHeatmap while drawing.

Usage

ccGenomicHeatmap(
  bed,
  col,
  na_col = "grey",
  numeric.column = NULL,
  border = NA,
  border_lwd = par("lwd"),
  border_lty = par("lty"),
  connection_height = mm_h(5),
  line_col = par("col"),
  line_lwd = par("lwd"),
  line_lty = par("lty"),
  heatmap_height = 0.15,
  side = c("inside", "outside"),
  track.margin = circos.par("track.margin")
)

Arguments

bed

A data frame in bed format, the matrix should be stored from the fourth column.

col

Colors for the heatmaps. The value can be a matrix or a color mapping function generated by colorRamp2.

na_col

Color for NA values.

numeric.column

Column index for the numeric columns. The values can be integer index or character index. By default it takes all numeric columns from the fourth column.

border

Border of the heatmap grids.

border_lwd

Line width for borders of heatmap grids.

border_lty

Line style for borders of heatmap grids.

connection_height

Height of the connection lines. If it is set to NULL, no connection will be drawn. Use mm_h/cm_h/inches_h to set a height in absolute unit.

line_col

Color of the connection lines. The value can be a vector.

line_lwd

Line width of the connection lines.

line_lty

Line style of the connection lines.

heatmap_height

Height of the heatmap track

side

Side of the heatmaps. Is the heatmap facing inside or outside?

track.margin

Bottom and top margins.

Value

Object ccGenomicTrack

Examples


library(circlizePlus)
cc = ccPlot(initMode = "initializeWithIdeogram")
bed = generateRandomBed(nr = 100, nc = 4)
col_fun = colorRamp2(c(-1, 0, 1), c("green", "black", "red"))
t1 = ccGenomicHeatmap(bed, col = col_fun, side = "inside", border = "white")
cc + t1
circos.clear()

Define an ideograms track for genomic graph

Description

Object ccGenomicTrack will call the function circlize::circos.genomicIdeogram while drawing.

Usage

ccGenomicIdeogram(
  cytoband = system.file(package = "circlize", "extdata", "cytoBand.txt"),
  species = NULL,
  track.height = mm_h(2),
  track.margin = circos.par("track.margin")
)

Arguments

cytoband

A data frame or a file path, pass to read.cytoband.

species

Abbreviations of the genome, pass to read.cytoband.

track.height

Height of the ideogram track.

track.margin

Margins for the track.

Value

Object ccGenomicTrack

Examples


library(circlizePlus)
cc = ccPlot(initMode = "initializeWithIdeogram",chromosome.index = "chr1", plotType = NULL)
human_cytoband = read.cytoband(species = "hg19")$df
t2=ccGenomicIdeogram(human_cytoband)
cc+t2
circos.clear()

Add labels to specific genomic track

Description

Object ccGenomicTrack will call the function circlize::circos.genomicLabels while drawing.

Usage

ccGenomicLabels(
  bed,
  labels = NULL,
  labels.column = NULL,
  facing = "clockwise",
  niceFacing = TRUE,
  col = par("col"),
  cex = 0.8,
  font = par("font"),
  padding = 0.4,
  connection_height = mm_h(5),
  line_col = par("col"),
  line_lwd = par("lwd"),
  line_lty = par("lty"),
  labels_height = NULL,
  side = c("inside", "outside"),
  labels.side = side,
  track.margin = circos.par("track.margin")
)

Arguments

bed

A data frame in bed format.

labels

A vector of labels corresponding to rows in bed.

labels.column

If the label column is already in bed, the index for this column in bed.

facing

fFacing of the labels. The value can only be "clockwise" or "reverse.clockwise".

niceFacing

Whether automatically adjust the facing of the labels.

col

Color for the labels.

cex

Size of the labels.

font

Font of the labels.

padding

Padding of the labels, the value is the ratio to the height of the label.

connection_height

Height of the connection track.

line_col

Color for the connection lines.

line_lwd

Line width for the connection lines.

line_lty

Line type for the connectioin lines.

labels_height

Height of the labels track.

side

Side of the labels track, is it in the inside of the track where the regions are marked?

labels.side

Same as side. It will replace side in the future versions.

track.margin

Bottom and top margins.

Value

Object ccGenomicTrack

Examples

library(circlizePlus)
bed = generateRandomBed(nr = 50, fun = function(k) sample(letters, k, replace = TRUE))
bed[1, 4] = "aaaaa"
cc = ccPlot(initMode = "initializeWithIdeogram", plotType = NULL)
t1 = ccGenomicLabels(bed, labels.column = 4, side = "outside",
                     col = as.numeric(factor(bed[[1]])), line_col = as.numeric(factor(bed[[1]])))
cc + t1
circos.clear()

Add lines for genomic data visualization

Description

Object ccGenomicCellGeom will call the function circlize::circos.genomicLines while drawing.

Usage

ccGenomicLines(
  region = NULL,
  value = NULL,
  numeric.column = NULL,
  posTransform = NULL,
  col = ifelse(area, "grey", "black"),
  lwd = par("lwd"),
  lty = par("lty"),
  type = "l",
  area = FALSE,
  area.baseline = NULL,
  border = "black",
  baseline = "bottom",
  pt.col = par("col"),
  cex = par("cex"),
  pch = par("pch"),
  ...
)

Arguments

region

A data frame contains 2 column which correspond to start positions and end positions.

value

A data frame contains values and other information.

numeric.column

Which column in value data frame should be taken as y-value. If it is not defined, the whole numeric columns in value will be taken.

posTransform

Self-defined function to transform genomic positions, see posTransform.default for explaination.

col

col of lines/areas. If there are more than one numeric column, the length of col can be either one or number of numeric columns. If there is only one numeric column and type is either segment or h, the length of col can be either one or number of rows of region. pass to circos.lines

lwd

Settings are similar as col. Pass to circos.lines.

lty

Settings are similar as col. Pass to circos.lines.

type

There is an additional option segment which plot segment lines from start position to end position. Settings are similar as col. Pass to circos.lines.

area

Settings are similar as col. Pass to circos.lines.

area.baseline

Deprecated, use baseline instead.

border

Settings are similar as col. Pass to circos.lines.

baseline

Settings are similar as col. Pass to circos.lines.

pt.col

Settings are similar as col. Pass to circos.lines.

cex

Settings are similar as col. Pass to circos.lines.

pch

Settings are similar as col. Pass to circos.lines.

...

Mysterious parameters.

Value

Object ccGenomicCellGeom

Examples

library(circlizePlus)
data <- generateRandomBed(nr = 30, nc = 2)
all_chr <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8",
"chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16",
"chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY")
cc <- ccPlot(initMode = "initializeWithIdeogram", plotType = NULL)
t1 <- ccGenomicTrack(data = data, numeric.column = 4)
cells1 <- ccCells(sector.indexes = all_chr) +
ccGenomicLines(numeric.column = 2)
t1 <- t1 + cells1
show(cc + t1)

Description

Object ccGenomicLink will call the function circlize::circos.genomicLink while drawing.

Usage

ccGenomicLink(
  region1,
  region2,
  rou = NULL,
  rou1 = rou,
  rou2 = rou,
  col = "black",
  lwd = par("lwd"),
  lty = par("lty"),
  border = col,
  ...
)

Arguments

region1

A data frame in bed format.

region2

A data frame in bed format.

rou

Pass to circos.link.

rou1

Pass to circos.link.

rou2

Pass to circos.link.

col

Pass to circos.link, length can be either one or nrow of region1.

lwd

Pass to circos.link, length can be either one or nrow of region1.

lty

Pass to circos.link, length can be either one or nrow of region1.

border

Pass to circos.link, length can be either one or nrow of region1.

...

Pass to circos.link.

Value

Object ccGenomicLink

Examples


library(circlizePlus)
set.seed(123)

bed1 = generateRandomBed(nr = 100)
bed1 = bed1[sample(nrow(bed1), 20), ]
bed2 = generateRandomBed(nr = 100)
bed2 = bed2[sample(nrow(bed2), 20), ]
par1 = ccPar("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
cc = ccPlot(initMode="initializeWithIdeogram")

link1 = ccGenomicLink(bed1, bed2, col = sample(1:5, 20, replace = TRUE), border = NA)
cc + par1 + link1

Description

S4 class ccGenomicLink

Slots

func

character. Normally it is "circos.genomicLink".

params

list. A named list that stores the parameters of the function circlize::circos.genomicLink called by the backend.

Examples

NULL

Add points for genomic data visualization

Description

Object ccGenomicCellGeom will call the function circlize::circos.genomicPoints while drawing.

Usage

ccGenomicPoints(
  region = NULL,
  value = NULL,
  numeric.column = NULL,
  posTransform = NULL,
  pch = par("pch"),
  col = par("col"),
  cex = par("cex"),
  bg = par("bg"),
  ...
)

Arguments

region

A data frame contains 2 columns which correspond to start positions and end positions.

value

A data frame contains values and other information.

numeric.column

Which column in value data frame should be taken as y-value. If it is not defined, the whole numeric columns in value will be taken.

posTransform

Self-defined function to transform genomic positions, see posTransform.default for explanation

pch

Type of points. Settings are similar as col. Pass to circos.points.

col

Color of points. If there is only one numeric column, the length of col can be either one or number of rows of region. If there are more than one numeric column, the length of col can be either one or number of numeric columns. Pass to circos.points.

cex

Size of points. Settings are similar as col. Pass to circos.points.

bg

Background colors for points.

...

Mysterious parameters.

Value

Object ccGenomicCellGeom

Examples

library(circlizePlus)
data <- generateRandomBed(nr = 30, nc = 2)
all_chr <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8",
"chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16",
"chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY")
cc <- ccPlot(initMode = "initializeWithIdeogram", plotType = NULL)
t1 <- ccGenomicTrack(data = data, numeric.column = 4)
cells1 <- ccCells(sector.indexes = all_chr) +
ccGenomicPoints(region = \(region, value){
  region
}, value = \(region, value){
  value
}, numeric.column = 2)
t1 <- t1 + cells1
show(cc + t1)

Create a rainfall plot

Description

Object ccGenomicTrack will call the function circlize::circos.genomicRainfall while drawing.

Usage

ccGenomicRainfall(
  data,
  mode = "min",
  ylim = NULL,
  col = "black",
  pch = par("pch"),
  cex = par("cex"),
  normalize_to_width = FALSE,
  ...
)

Arguments

data

A bed-file-like data frame or a list of data frames.

mode

How to calculate the distance of two neighbouring regions, pass to rainfallTransform.

ylim

ylim for rainfall plot track. If normalize_to_width is FALSE, the value should correspond to log10(dist+1), and if normalize_to_width is TRUE, the value should correspond to log2(rel_dist).

col

Color of points. It should be length of one. If data is a list, the length of col can also be the length of the list.

pch

Style of points.

cex

Size of points.

normalize_to_width

If it is TRUE, the value is the relative distance divided by the width of the region.

...

Pass to circos.trackPlotRegion.

Value

Object ccGenomicTrack

Examples


library(circlizePlus)
load(system.file(package = "circlize", "extdata", "DMR.RData"))
cc = ccPlot(initMode="initializeWithIdeogram", chromosome.index = paste0("chr", 1:22))
bed_list = list(DMR_hyper, DMR_hypo)
t1 = ccGenomicRainfall(bed_list, pch = 16, cex = 0.4, col = c("#FF000080", "#0000FF80"))
cc + t1
circos.clear()

Draw rectangle for genomic data visualization

Description

Object ccGenomicCellGeom will call the function circlize::circos.genomicRect while drawing.

Usage

ccGenomicRect(
  region = NULL,
  value = NULL,
  ytop = NULL,
  ybottom = NULL,
  ytop.column = NULL,
  ybottom.column = NULL,
  posTransform = NULL,
  col = NA,
  border = "black",
  lty = par("lty"),
  ...
)

Arguments

region

A data frame contains 2 column which correspond to start positions and end positions.

value

A data frame contains values and other information.

ytop

A vector or a single value indicating top position of rectangles.

ybottom

A vector or a single value indicating bottom position of rectangles.

ytop.column

If ytop is in value, the index of the column.

ybottom.column

If ybottom is in value, the index of the column.

posTransform

Self-defined function to transform genomic positions, see posTransform.default for explaination.

col

The length of col can be either one or number of rows of region. Pass to circos.rect.

border

Settings are similar as col. Pass to circos.rect.

lty

Settings are similar as col. Pass to circos.rect.

...

Mysterious parameters.

Value

Object ccGenomicCellGeom

Examples

library(circlizePlus)
par1 <- ccPar("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
cc <- ccPlot(initMode = "initializeWithIdeogram", plotType = NULL)
bed1 <- generateRandomBed(nr = 100)
bed2 <- generateRandomBed(nr = 100)
bed_list <- list(bed1, bed2)
f <- colorRamp2(breaks = c(-1, 0, 1), colors = c("green", "black", "red"))
track1 <- ccGenomicTrack(data = bed_list, stack = TRUE)
all_chr <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8",
"chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16",
"chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY")
rect1 <- ccGenomicRect(col = 1, border = NA)
cells1 <- ccCells(sector.indexes = all_chr) + rect1
cc + par1 + (track1 + cells1)

Add text for genomic data visualization

Description

Object ccGenomicCellGeom will call the function circlize::circos.genomicText while drawing.

Usage

ccGenomicText(
  region = NULL,
  value = NULL,
  y = NULL,
  labels = NULL,
  labels.column = NULL,
  numeric.column = NULL,
  posTransform = NULL,
  direction = NULL,
  facing = "inside",
  niceFacing = FALSE,
  adj = par("adj"),
  cex = 1,
  col = "black",
  font = par("font"),
  padding = 0,
  extend = 0,
  align_to = "region",
  ...
)

Arguments

region

A data frame contains 2 column which correspond to start positions and end positions.

value

A data frame contains values and other information.

y

A vector or a single value indicating position of text.

labels

Labels of text corresponding to each genomic positions.

labels.column

If labels are in value, index of column in value.

numeric.column

Which column in value data frame should be taken as y-value. If it is not defined, only the first numeric columns in value will be taken.

posTransform

Self-defined function to transform genomic positions, see posTransform.default for explanation.

direction

Deprecated, use facing instead.

facing

Passing to circos.text. Settings are similar as col.

niceFacing

Should the facing of text be adjusted to fit human eyes?

adj

Pass to circos.text. Settings are similar as col.

cex

Pass to circos.text. Settings are similar as col.

col

Pass to circos.text. The length of col can be either one or number of rows of region.

font

Pass to circos.text. Settings are similar as col.

padding

pass to posTransform if it is set as posTransform.text.

extend

pass to posTransform if it is set as posTransform.text.

align_to

pass to posTransform if it is set as posTransform.text.

...

Mysterious parameters.

Value

Object ccGenomicCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(initMode = "initializeWithIdeogram", plotType = NULL)
bed <- generateRandomBed(nr = 20)
track1 <- ccGenomicTrack(data = bed, ylim = c(0, 1))
all_chr <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8",
"chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16",
"chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY")
text1 <- ccGenomicText(y = 0.5, labels = "text")
cells1 <- ccCells(sector.indexes = all_chr) + text1
cc + (track1 + cells1)

Define a track for genomic data visualization

Description

Object ccGenomicTrack will call the function circlize::circos.genomicTrackPlotRegion while drawing.

Usage

ccGenomicTrack(
  data = NULL,
  ylim = NULL,
  stack = FALSE,
  numeric.column = NULL,
  jitter = 0,
  panel.fun = function(region, value, ...) {
     NULL
 },
  ...
)

Arguments

data

A bed-file-like data frame or a list of data frames

ylim

If it is NULL, the value will be calculated from data. If stack is set to TRUE, this value is ignored.

stack

whether to plot in a "stack" mode.

numeric.column

Columns of numeric values in data that will be used for plotting. If data is a data frame list, numeric.column should be either length of one or length of data. If value of numeric.column is not set, its value will depend on the structure of data. If data is a data frame, the default value for numeric.column is all the numeric column starting from the fourth column. If data is a list of data frame, the default value for numeric.column is a vector which have the same length as data and the value in default numeric.column is the index of the first numeric column in corresponding data frame.

jitter

Numeric. Only works for adding points in circos.genomicTrackPlotRegion under stack mode

panel.fun

Self-defined function which will be applied on each sector. Please not it is different from that in circos.trackPlotRegion. In this function, there are two arguments (region and value) plus .... In them, region is a two-column data frame with start positions and end positions in current genomic category (e.g. chromosome). value is a data frame which is derived from data but excluding the first three columns. Rows in value correspond to rows in region. ... is mandatory and is used to pass internal parameters to other functions. The definition of value will be different according to different input data (data frame or list of data frame) and different settings (stacked or not), please refer to 'details' section and vignettes to detailed explanation.

...

Pass to circos.trackPlotRegion.

Value

Object ccGenomicTrack

Examples

library(circlizePlus)
cc = ccPlot(initMode = "initializeWithIdeogram",chromosome.index = "chr1", plotType = NULL)
bed = generateRandomBed(nr = 300)
t1 = ccGenomicTrack(bed, panel.fun = function(region, value, ...) {
  circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
cc+t1
circos.clear()

S4 class ccGenomicTrack

Description

S4 class ccGenomicTrack

Slots

func

character. Normally it is "circos.genomicTrack" or "circos.genomicIdeogram" or "circos.genomicHeatmap" or "circos.genomicLabels" or"circos.genomicRainfall" or "circos.genomicDensity".

params

list. A named list that stores the parameters of the function called by the backend.

trackGeoms

list. A list where ccTrackGeom are stored.

cells

list. A list where ccCell are stored.

Examples

library(circlizePlus)
cc = ccPlot(initMode = "initializeWithIdeogram",chromosome.index = "chr1", plotType = NULL)
bed = generateRandomBed(nr = 300)
t1 = ccGenomicTrack(bed, panel.fun = function(region, value, ...) {
  circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
cc+t1
circos.clear()

Object generator for S4 class ccHeatmap

Description

Object ccHeatmap will call the function circlize::circos.heatmap while drawing.

Usage

ccHeatmap(
  mat,
  split = NULL,
  col,
  na.col = "grey",
  cell.border = NA,
  cell.lty = 1,
  cell.lwd = 1,
  bg.border = NA,
  bg.lty = par("lty"),
  bg.lwd = par("lwd"),
  ignore.white = is.na(cell.border),
  cluster = TRUE,
  clustering.method = "complete",
  distance.method = "euclidean",
  dend.callback = function(dend, m, si) reorder(dend, rowMeans(m)),
  dend.side = c("none", "outside", "inside"),
  dend.track.height = 0.1,
  rownames.side = c("none", "outside", "inside"),
  rownames.cex = 0.5,
  rownames.font = par("font"),
  rownames.col = "black",
  show.sector.labels = FALSE,
  cell_width = rep(1, nrow(mat)),
  clear = TRUE,
  ...
)

Arguments

mat

A matrix or a vector. The vector is transformed as a one-column matrix.

split

A categorical variable. It splits the matrix into a list of matrices.

col

If the values in the matrices are continuous, the color should be a color mapping generated by colorRamp2. If the values are characters, the color should be a named color vector.

na.col

Color for NA values.

cell.border

Border color of cells. A single scalar.

cell.lty

Line type of cell borders. A single scalar.

cell.lwd

Line width of cell borders. A single scalar.

bg.border

Color for background border.

bg.lty

Line type of the background border.

bg.lwd

Line width of the background border.

ignore.white

Whether to draw the white color?

cluster

whether to apply clustering on rows. The value can also be a dendrogram/hclust object or other objects that can be converted to with as.dendrogram.

clustering.method

Clustering method, pass to hclust.

distance.method

Distance method, pass to dist.

dend.callback

A callback function that is applied to the dendrogram in every sector.

dend.side

Side of the dendrograms relative to the heatmap track.

dend.track.height

Track height of the dendrograms.

rownames.side

Side of the row names relative to the heatmap track.

rownames.cex

Cex of row names.

rownames.font

Font of row names.

rownames.col

Color of row names.

show.sector.labels

Whether to show sector labels.

cell_width

Relative widths of heatmap cells.

clear

Whether to call circlize::circos.clear before drawing.

...

Pass to circos.track which draws the heatmap track.

Value

Object ccHeatmap

Examples


library(circlizePlus)
set.seed(123)
mat1 <- rbind(
  cbind(
    matrix(rnorm(50 * 5, mean = 1), nr = 50),
    matrix(rnorm(50 * 5, mean = -1), nr = 50)
  ),
  cbind(
    matrix(rnorm(50 * 5, mean = -1), nr = 50),
    matrix(rnorm(50 * 5, mean = 1), nr = 50)
  )
)
rownames(mat1) <- paste0("R", 1:100)
colnames(mat1) <- paste0("C", 1:10)
mat1 <- mat1[sample(100, 100), ] # randomly permute rows
split <- sample(letters[1:5], 100, replace = TRUE)
split <- factor(split, levels = letters[1:5])
col_fun1 <- colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))
ccHeatmap(mat = mat1, split = split, col = col_fun1)

S4 class ccHeatmap

Description

ccHeatmap is a special class. It can be used not only as a single track but also as the result of adding a heatmap track to a ccPlot

Slots

func

character. Normally it is "circos.heatmap".

params

list. A named list that stores the parameters of the function circlize::circos.heatmap called by the backend.

trackGeoms

list. A list where ccTrackGeom are stored.

cells

list. A list where ccCell are stored.

tracks

list. A list where ccTrack or ccGenomicTrack or ccHeatmap are stored.

links

list. A list where ccLink or ccGenomicLink or ccHeatmapLink are stored.

pars

list. A list where ccPar are stored.

clear

logical. Whether to call circlize::circos.clear before drawing.

Description

Object ccHeatmapLink will call the function circlize::circos.heatmap.link while drawing.

Usage

ccHeatmapLink(row_from, row_to, ...)

Arguments

row_from

The row index where the link starts. The value should be length 1. If you want to draw multiple links, put the function in a for loop.

row_to

The row index where the link ends.

...

Pass to circos.link.

Value

Object ccHeatmapLink

Examples


library(circlizePlus)
set.seed(123)
mat = matrix(rnorm(100*10), nrow = 100)
rownames(mat) = paste0("R", 1:100)
col_fun = colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))
cc = ccHeatmap(mat, col = col_fun, rownames.side = "outside")
link1 = ccHeatmapLink(10, 60)
cc + link1

Description

S4 class ccHeatmapLink

Slots

func

character. Normally it is "circos.heatmap.link".

params

list. A named list that stores the parameters of the function circlize::circos.heatmap.link called by the backend.

Examples

NULL

Draw lines in a region

Description

Object ccCellGeom will call the function circlize::circos.lines while drawing.

Usage

ccLines(
  x = NULL,
  y = NULL,
  col = ifelse(area, "grey", par("col")),
  lwd = par("lwd"),
  lty = par("lty"),
  type = "l",
  straight = FALSE,
  area = FALSE,
  area.baseline = NULL,
  border = "black",
  baseline = "bottom",
  pt.col = par("col"),
  cex = par("cex"),
  pch = par("pch")
)

Arguments

x

Data points on x-axis, measured in "current" data coordinate.

y

Data points on y-axis, measured in "current" data coordinate.

col

Line color.

lwd

Line width.

lty

Line style.

type

Line type, similar as type argument in lines, but only in c("l", "o", "h", "s")

straight

Whether draw straight lines between points.

area

Whether to fill the area below the lines. If it is set to TRUE, col controls the filled color in the area and border controls color of the line.

area.baseline

deprecated, use baseline instead.

border

color for border of the area.

baseline

The base line to draw areas. By default it is the minimal of y-range (bottom). It can be a string or a number. If a string, it should be one of bottom and top. This argument also works if type is set to h.

pt.col

If type is "o", point color.

cex

If type is "o", point size.

pch

If type is "o", point type.

Value

Object ccCellGeom

Examples

library(circlizePlus)
sectors <- letters[1:9]
par <- ccPar(points.overflow.warning = FALSE)
cc <- ccPlot(sectors = sectors, xlim = c(0, 10))
cc <- cc + par
track <- ccTrack(sectors = sectors, ylim = c(0, 10), track.height = 0.5)
cells <- ccCell(sector.index = "a") + ccLines(sort(x = runif(10) * 10), y = runif(10) * 10)
track <- track + cells
cc + track

Description

Object ccLink will call the function circlize::circos.link while drawing.

Usage

ccLink(
  sector.index1,
  point1,
  sector.index2,
  point2,
  rou = NULL,
  rou1 = rou,
  rou2 = rou,
  h = NULL,
  h.ratio = 0.5,
  w = 1,
  h2 = h,
  w2 = w,
  inverse = FALSE,
  col = "black",
  lwd = par("lwd"),
  lty = par("lty"),
  border = col,
  directional = 0,
  arr.length = ifelse(arr.type == "big.arrow", 0.02, 0.4),
  arr.width = arr.length/2,
  arr.type = "triangle",
  arr.lty = lty,
  arr.lwd = lwd,
  arr.col = col,
  reduce_to_mid_line = FALSE
)

Arguments

sector.index1

Index for the first sector where one link end locates

point1

A single value or a numeric vector of length 2. If it is a 2-elements vector, then the link would be a belt/ribbon.

sector.index2

Index for the other sector where the other link end locates

point2

A single value or a numeric vector of length 2. If it is a 2-elements vector, then the link would be a belt/ribbon.

rou

The position of the the link ends (if rou1 and rou2 are not set). It is the percentage of the radius of the unit circle. By default its value is the position of bottom margin of the most inner track.

rou1

The position of end 1 of the link.

rou2

The position of end 2 of the link.

h

Height of the link, measured as percent to the radius to the unit circle. By default it is automatically infered.

h.ratio

systematically change the link height. The value is between 0 and 1.

w

Since the link is a Bezier curve, it controls the shape of Bezier curve.

h2

Height of the bottom edge of the link if it is a ribbon.

w2

Shape of the bottom edge of the link if it is a ribbon.

inverse

Whether the link is inversed.

col

Color of the link. If the link is a ribbon, then it is the filled color for the ribbon.

lwd

Line (or border) width

lty

Line (or border) style

border

If the link is a ribbon, then it is the color for the ribbon border.

directional

0 for no direction, 1 for direction from point1 to point2, -1 for direction from point2 to point1. 2 for two directional. The direction is important when arrow heads are added.

arr.length

Length of the arrows, measured in 'cm', pass to Arrowhead. If arr.type is set to big.arrow, the value is percent to the radius of the unit circle.

arr.width

Width of the arrows, pass to Arrowhead.

arr.type

Type of the arrows, pass to Arrowhead. Default value is triangle. There is an additional option big.arrow.

arr.lty

Line type of arrows, pass to Arrowhead.

arr.lwd

Line width of arrows, pass to Arrowhead.

arr.col

Color of the arrows, pass to Arrowhead.

reduce_to_mid_line

Only use the middle points of point1 and point2 to draw the link.

Value

Object ccLink

Examples

library(circlizePlus)
set.seed(999)
n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),x = rnorm(n), y = runif(n))
cc = ccPlot(initMode = "initialize", sectors = df$sectors, x = df$x)
track1 = ccTrack(df$sectors, y = df$y)
col = rep(c("#FF0000", "#00FF00"), 4)
tPoint1 = ccTrackPoints(df$sectors, df$x, df$y, col = col, pch = 16, cex = 0.5)
link1 = ccLink("a", 0, "b", 0, h = 0.4)
link2 = ccLink("c", c(-0.5, 0.5), "d", c(-0.5,0.5), col = "red",border = "blue", h = 0.2)
link3 = ccLink("e", 0, "g", c(-1,1), col = "green", border = "black", lwd = 2, lty = 2)
cc + (track1 + tPoint1) + link1 + link2 + link3

Description

S4 class ccLink

Slots

func

character. Normally it is "circos.link".

params

list. A named list that stores the parameters of the function circlize::circos.link called by the backend.

Examples

NULL

Parameters for the circular layout

Description

Object ccPar will call the function circlize::circos.par while drawing.

Usage

ccPar(...)

Arguments

...

Arguments passed on to circlize::circos.par

RESET

reset to default values

READ.ONLY

please ignore

LOCAL

please ignore

ADD

please ignore

Value

Object ccPar

Examples

library(circlizePlus)
set.seed(999)
n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),x = rnorm(n), y = runif(n))
par1 = ccPar("track.height" = 0.1)
cc = ccPlot(initMode = "initialize", sectors = df$sectors, x = df$x)
track1 = ccTrack(df$sectors, y = df$y)
col = rep(c("#FF0000", "#00FF00"), 4)
tPoint1 = ccTrackPoints(df$sectors, df$x, df$y, col = col, pch = 16, cex = 0.5)
cc + par1 + (track1 + tPoint1)

Object generator for S4 class ccPar

Description

Object generator for S4 class ccPar

Slots

params

params list. A named list that stores the parameters of the function circlize::circos.par called by the backend.

Examples

NULL

Object generator for S4 class ccPlot

Description

Object ccPlot calls one of the following functions based on the value of initMode: circlize::circos.initialize, circlize::circos.genomicInitialize, circlize::circos.initializeWithIdeogram, circlize::circos.heatmap.initialize.
The correct way to call it is as follows:
ccPlot(initMode = 'initialize',clear = TRUE,sectors = NULL,x = NULL,xlim = NULL,sector.width = NULL,factors = sectors,ring = FALSE)

ccPlot(initMode = 'genomicInitialize',clear = TRUE,data=NULL,sector.names = NULL,major.by = NULL,plotType = c("axis", "labels"),tickLabelsStartFromZero = TRUE,axis.labels.cex = 0.4*par("cex"),labels.cex = 0.8*par("cex"),track.height = NULL,...)

ccPlot(initMode = 'initializeWithIdeogram',clear = TRUE,cytoband = system.file(package = "circlize", "extdata", "cytoBand.txt"),species = NULL,sort.chr = TRUE,chromosome.index = usable_chromosomes(species),major.by = NULL,plotType = c("ideogram", "axis", "labels"),track.height = NULL,ideogram.height = convert_height(2, "mm"),...)

ccPlot(initMode = 'heatmap.initialize',clear = TRUE,mat=NULL, split = NULL, cluster = TRUE,clustering.method = "complete", distance.method = "euclidean",dend.callback = function(dend, m, si) reorder(dend, rowMeans(m)),cell_width = rep(1, nrow(mat)))

Usage

ccPlot(initMode = "initialize", clear = TRUE, ...)

Arguments

initMode

It can only be the following values: "initialize", "genomicInitialize", "initializeWithIdeogram", "heatmap.initialize".

clear

Whether to call circlize::circos.clear before drawing.

...

Arguments passed on to circlize::circos.initialize, circlize::circos.genomicInitialize, circlize::circos.initializeWithIdeogram, circlize::circos.heatmap.initialize

sectors

A factor variable or a character vector which represent data categories

factors

The same as sectors. It will be removed in future versions.

x

Data on x-axes, a vector

xlim

Ranges for values on x-axes, see "details" section for explanation of the format

sector.width

Width for each sector. The length of the vector should be either 1 which means all sectors have same width or as same as the number of sectors. Values for the vector are relative, and they will be scaled by dividing their summation. By default, it is NULL which means the width of sectors correspond to the data range in sectors.

ring

Whether the sector represented as a ring. If yes, there should only be one sector in the circle.

data

A data frame in bed format.

sector.names

Labels for each sectors which will be drawn along each sector. It will not modify values of sector index.

major.by

Increment of major ticks. It is calculated automatically if the value is not set (about every 10 degrees there is a major tick).

plotType

If it is not NULL, there will create a new track containing axis and names for sectors. This argument controls which part should be drawn, axis for genomic axis and labels for chromosome names

tickLabelsStartFromZero

Whether axis tick labels start from 0? This will only affect the axis labels while not affect x-values in cells.

axis.labels.cex

The font size for the axis tick labels.

labels.cex

The font size for the labels.

track.height

If PlotType is not NULL, height of the annotation track.

cytoband

A path of the cytoband file or a data frame that already contains cytoband data. By default it is cytoband for hg19. Pass to read.cytoband.

species

Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this value is specified, the function will download cytoBand.txt.gz from UCSC website automatically. If there is no cytoband for user's species, it will keep on trying to download chromInfo file. Pass to read.cytoband or read.chromInfo.

chromosome.index

subset of chromosomes, also used to reorder chromosomes.

sort.chr

Whether chromosome names should be sorted (first sort by numbers then by letters). If chromosome.index is set, this argumetn is enforced to FALSE

ideogram.height

Height of the ideogram track

mat

A matrix or a vector. The vector is transformed as a one-column matrix.

split

A categorical variable. It splits the matrix into a list of matrices.

cluster

whether to apply clustering on rows. The value can also be a dendrogram/hclust object or other objects that can be converted to with as.dendrogram.

clustering.method

Clustering method, pass to hclust.

distance.method

Distance method, pass to dist.

dend.callback

A callback function that is applied to the dendrogram in every sector.

cell_width

Relative widths of heatmap cells.

Value

Object ccPlot

Examples

n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),
                x = rnorm(n), y = runif(n))
library(circlizePlus)
cc=ccPlot(initMode = 'initialize', sectors = df$sectors, x = df$x)

S4 class ccPlot

Description

S4 class ccPlot

Slots

initMode

character. It can only be the following values: "initialize", "genomicInitialize", "initializeWithIdeogram", "heatmap.initialize".

initParams

list. A named list that stores the parameters of the function called by the backend. Based on the value of initMode, the backend function will be one of the following four:circlize::circos.initialize, circlize::circos.genomicInitialize, circlize::circos.initializeWithIdeogram, circlize::circos.heatmap.initialize.

tracks

list. A list where ccTrack or ccGenomicTrack or ccHeatmap are stored.

links

list. A list where ccLink or ccGenomicLink or ccHeatmapLink are stored.

pars

list. A list where ccPar are stored.

clear

logical. Whether to call circlize::circos.clear before drawing.

Examples

n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),
                x = rnorm(n), y = runif(n))
library(circlizePlus)
cc=ccPlot(initMode = 'initialize', sectors = df$sectors, x = df$x)

Draw points in a region

Description

Object ccCellGeom will call the function circlize::circos.points while drawing.

Usage

ccPoints(
  x = NULL,
  y = NULL,
  pch = par("pch"),
  col = par("col"),
  cex = par("cex"),
  bg = par("bg")
)

Arguments

x

Data points on x-axis, measured in "current" data coordinate

y

Data points on y-axis, measured in "current" data coordinate

pch

Point type

col

Point color

cex

Point size

bg

backgrond of points

Value

Object ccCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(sectors = letters[1:8], xlim = c(0, 1))
track1 <- ccTrack(ylim = c(0, 1), panel.fun = function(x, y) {
  circos.points(runif(10), runif(10))
})
cells <- ccCell(sector.index = "a") + ccPoints(
  x = runif(10), y = runif(10),
   pch = 16, col = "red"
)
track1 <- track1 + cells
cc + track1

Draw polygon

Description

Object ccCellGeom will call the function circlize::circos.polygon while drawing.

Usage

ccPolygon(x = NULL, y = NULL, ...)

Arguments

x

Data points on x-axis

y

Data points on y-axis

...

pass to polygon

Value

Object ccCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(sectors = letters[1:8], xlim = c(0, 1))
track <- ccTrack(ylim = c(0, 10))
cell <- ccCell(sector.index = "a") + ccPolygon(x = c(0.5, 0.7, 1), y = c(2, 6, 8))
track <- track + cell
cc + track

Add raster image

Description

Object ccCellGeom will call the function circlize::circos.raster while drawing.

Usage

ccRaster(
  image,
  x,
  y,
  width,
  height,
  facing = c("inside", "outside", "reverse.clockwise", "clockwise", "downward",
    "bending.inside", "bending.outside"),
  niceFacing = FALSE,
  scaling = 1
)

Arguments

image

A raster object, or an object that can be converted by as.raster.

x

Position of the center of the raster image, measued in the data coordinate in the cell.

y

Position of the center of the raster image, measued in the data coordinate in the cell.

width

Width of the raster image. When facing is one of "inside", "outside", "clockwise" and "reverse.clockwise", the image should have absolute size where the value of width should be specified like 20mm, 1cm or 0.5inche. When facing is one of bending.inside and bending.outside, the value of width is measured in the data coordinate in the cell.

height

Height of the raster image. Same format as width. If the value of height is omit, default height is calculated by taking the aspect ratio of the original image. But when facing is one of bending.inside and bending.outside, height is mandatory to set.

facing

Facing of the raster image.

niceFacing

Facing of text. Please refer to vignette for different settings.

scaling

Scaling factor to resize the raster image.

Value

Object ccCellGeom

Examples


library(circlizePlus)
library(png)
image <- system.file("extdata", "Rlogo.png", package = "circlize")
image <- as.raster(readPNG(image))
library(circlizePlus)
cc <- ccPlot(sectors = letters[1:4], xlim = c(0, 10))
track <- ccTrack(ylim = c(0, 1))
cell <- ccCell(sector.index = "a") + ccRaster(image = image, x = 5, y = 0.5,
width = "2cm", height = "2cm", facing = "inside", niceFacing = TRUE)
track <- track + cell
cc + track

Draw rectangle in a region

Description

Object ccCellGeom will call the function circlize::circos.rect while drawing.

Usage

ccRect(xleft = NULL, ybottom = NULL, xright = NULL, ytop = NULL, rot = 0, ...)

Arguments

xleft

x for the left bottom points

ybottom

y for the left bottom points

xright

x for the right top points

ytop

y for the right top points

rot

Rotation of the rectangles. The value is measured clockwise in degree. Rotation is relative to the center of the rectangles.

...

pass to polygon

Value

Object ccCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(sectors = letters[1:8], xlim = c(0, 1))
track <- ccTrack(ylim = c(0, 1), track.height = 0.3)
cell <- ccCell(sector.index = "a") + ccRect(xleft = 0.7, ybottom = 0.1, xright = 0.8, ytop = 0.9)
track <- track + cell
cc + track

Draw segments connecting points in a region

Description

Object ccCellGeom will call the function circlize::circos.segments while drawing.

Usage

ccSegments(
  x0 = NULL,
  y0 = NULL,
  x1 = NULL,
  y1 = NULL,
  straight = FALSE,
  col = par("col"),
  lwd = par("lwd"),
  lty = par("lty"),
  ...
)

Arguments

x0

x coordinates for starting points.

y0

y coordinates for ending points.

x1

x coordinates for starting points.

y1

y coordinates for ending points.

straight

Whether the segment is a straight line.

col

Color of the segments.

lwd

Line width of the segments.

lty

Line type of the segments.

...

Pass to lines.

Value

Object ccCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(sectors = letters[1:8], xlim = c(0, 1))
track <- ccTrack(ylim = c(0, 1), track.height = 0.3)
cell <- ccCell(sector.index = "a") + ccSegments(x0 = 0.7, y0 = 0.1, x1 = 0.7, y1 = 0.9)
track <- track + cell
cc + track

Draw text in a cell

Description

Object ccCellGeom will call the function circlize::circos.text while drawing.

Usage

ccText(
  x = NULL,
  y = NULL,
  labels,
  direction = NULL,
  facing = c("inside", "outside", "reverse.clockwise", "clockwise", "downward",
    "bending", "bending.inside", "bending.outside"),
  niceFacing = FALSE,
  adj = par("adj"),
  cex = 1,
  col = par("col"),
  font = par("font"),
  ...
)

Arguments

x

Data points on x-axis

y

Data points on y-axis

labels

Labels for each points

direction

deprecated, use facing instead.

facing

Facing of text. Please refer to vignette for different settings

niceFacing

Should the facing of text be adjusted to fit human eyes?

adj

offset for text. By default the text position adjustment is either horizontal or vertical in the canvas coordinate system. The "circular horizontal" offset can be set as a value in degree unit and the value should be wrapped by degree.

cex

Font size

col

Font color

font

Font style

...

Pass to text

Value

Object ccCellGeom

Examples

library(circlizePlus)
n <- 1000
df <- data.frame(
  sectors = sample(letters[1:8], n, replace = TRUE),
  x = rnorm(n), y = runif(n)
)
par1 <- ccPar("track.height" = 0.1)
cc <- ccPlot(sectors = df$sectors, x = df$x) + par1
track1 <- ccTrack(
  sectors = df$sectors, y = df$y,
  panel.fun = function(x, y) {
    circos.text(
      CELL_META$xcenter,
      CELL_META$cell.ylim[2] + mm_y(5),
      CELL_META$sector.index
    )
    circos.axis(labels.cex = 0.6)
  }
)
cell1 <- ccCell(sector.index = "a") + ccText(-1, 0.5, "text")
track1 <- track1 + cell1
cc <- cc + track1
cc

Define a generic track

Description

Object ccTrack will call the function circlize::circos.trackPlotRegion while drawing.

Usage

ccTrack(
  sectors = NULL,
  x = NULL,
  y = NULL,
  ylim = NULL,
  force.ylim = TRUE,
  track.index = NULL,
  track.height = circos.par("track.height"),
  track.margin = circos.par("track.margin"),
  cell.padding = circos.par("cell.padding"),
  bg.col = NA,
  bg.border = "black",
  bg.lty = par("lty"),
  bg.lwd = par("lwd"),
  panel.fun = function(x, y) {
     NULL
 },
  factors = sectors
)

Arguments

sectors

A factor or a character vector which represents categories of data, if it is NULL, then it uses all sector index.

x

Data on x-axis. It is only used if panel.fun is set.

y

Data on y-axis

ylim

Range of data on y-axis

force.ylim

Whether to force all cells in the track to share the same ylim. Normally, all cells on a same track should have same ylim.

track.index

Index for the track which is going to be created/updated. If the specified track has already been created, this function just updated corresponding track with new plot. If the specified track is NULL or has not been created, this function just creates it. Note the value for this argument should not exceed maximum track index plus 1.

track.height

Height of the track. It is the percentage to the radius of the unit circles. The value can be set by uh to an absolute unit. If updating a track (with proper track.index value), this argument is ignored.

track.margin

only affect current track

cell.padding

only affect current track

bg.col

Background color for the plotting regions. It can be vector which has the same length of sectors.

bg.border

Color for the border of the plotting regions. It can be vector which has the same length of sectors.

bg.lty

Line style for the border of the plotting regions. It can be vector which has the same length of sectors.

bg.lwd

Line width for the border of the plotting regions. It can be vector which has the same length of sectors.

panel.fun

Panel function to add graphics in each cell, see "details" section and vignette for explanation.

factors

The same as sectors. It will be removed in future versions.

Value

Object ccTrack

Examples

library(circlizePlus)
n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),
                x = rnorm(n), y = runif(n))
library(circlizePlus)
par1=ccPar("track.height" = 0.1)
cc=ccPlot(sectors = df$sectors, x = df$x) + par1
track1 = ccTrack(sectors = df$sectors, y = df$y,
                 panel.fun = function(x, y) {
                   circos.text(CELL_META$xcenter,
                               CELL_META$cell.ylim[2] + mm_y(5),
                               CELL_META$sector.index)
                   circos.axis(labels.cex = 0.6)
                 })
cc=cc+track1
cc
circos.clear()

S4 class ccTrack

Description

S4 class ccTrack

Slots

func

character. Normally it is "circos.track" or "circos.trackHist".

params

list. A named list that stores the parameters of the function called by the backend.

trackGeoms

list. A list where ccTrackGeom are stored.

cells

list. A list where ccCell are stored.

Examples

n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),
                x = rnorm(n), y = runif(n))
library(circlizePlus)
par1=ccPar("track.height" = 0.1)
cc=ccPlot(sectors = df$sectors, x = df$x) + par1
track1 = ccTrack(sectors = df$sectors, y = df$y,
                 panel.fun = function(x, y) {
                   circos.text(CELL_META$xcenter,
                               CELL_META$cell.ylim[2] + mm_y(5),
                               CELL_META$sector.index)
                   circos.axis(labels.cex = 0.6)
                 })
cc=cc+track1
cc
circos.clear()

S4 class ccTrackGeom

Description

Objectified representation of the R package circlize's plotting functions and corresponding parameters at the track level.

Slots

func

character. The name of the plot function in the R package circlize.

params

list. A named list that stores the parameters of the function called by the backend.

Examples

NULL

Define a track of histograms

Description

Object ccTrack will call the function circlize::circos.trackHist while drawing.

Usage

ccTrackHist(
  sectors,
  x,
  track.height = circos.par("track.height"),
  track.index = NULL,
  ylim = NULL,
  force.ylim = TRUE,
  col = ifelse(draw.density, "black", NA),
  border = "black",
  lty = par("lty"),
  lwd = par("lwd"),
  bg.col = NA,
  bg.border = "black",
  bg.lty = par("lty"),
  bg.lwd = par("lwd"),
  breaks = "Sturges",
  include.lowest = TRUE,
  right = TRUE,
  draw.density = FALSE,
  bin.size = NULL,
  area = FALSE,
  factors = sectors
)

Arguments

sectors

A factor or a character vector which represents the categories of data

x

Data on the x-axis

track.height

Height of the track. It is the percentage to the radius of the unit circle. If to update a track, this argument is disabled.

track.index

Index for the track which is going to be updated. Setting it to NULL means creating the plotting regions in the next newest track.

ylim

Ranges on y-direction. By default, ylim is calculated automatically.

force.ylim

Whether to force all cells in the track to share the same ylim.

col

Filled color for histogram

border

Border color for histogram

lty

Line style for histogram

lwd

Line width for histogram

bg.col

Background color for the plotting regions

bg.border

Color for the border of the plotting regions

bg.lty

Line style for the border of the plotting regions

bg.lwd

Line width for the border of the plotting regions

breaks

see hist

include.lowest

see hist

right

see hist

draw.density

whether draw density lines instead of histogram bars.

bin.size

size of the bins of the histogram

area

whether to fill the area below the density lines. If it is set to TRUE, col controls the filled color in the area and border controls color of the line.

factors

The same as sectors. It will be removed in future versions.

Value

Object ccTrack

Examples

library(circlizePlus)
n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),
                x = rnorm(n), y = runif(n))
library(circlizePlus)
par1=ccPar("track.height" = 0.1)
cc=ccPlot(sectors = df$sectors, x = df$x) + par1;bgcol = rep(c("#EFEFEF", "#CCCCCC"), 4)
track2 = ccTrackHist(df$sectors, df$x, bin.size = 0.2, bg.col = bgcol, col = NA)
cc=cc+track2
cc
circos.clear()

Add lines on all sections of a single track.

Description

Object ccTrackGeom will call the function circlize::circos.trackLines while drawing.

Usage

ccTrackLines(
  sectors,
  x,
  y,
  col = par("col"),
  lwd = par("lwd"),
  lty = par("lty"),
  type = "l",
  straight = FALSE,
  area = FALSE,
  area.baseline = NULL,
  border = "black",
  baseline = "bottom",
  pt.col = par("col"),
  cex = par("cex"),
  pch = par("pch"),
  factors = sectors
)

Arguments

sectors

A factor or a character vector which represents the categories of data.

x

Data points on x-axis.

y

Data points on y-axis.

col

Line color.

lwd

Line width.

lty

Line style.

type

Line type, similar as type argument in lines, but only in c("l", "o", "h", "s").

straight

Whether draw straight lines between points.

area

Whether to fill the area below the lines. If it is set to TRUE, col controls the filled color in the area and border controls the color of the line.

area.baseline

Deprecated, use baseline instead.

border

Color for border of the area.

baseline

The base line to draw area, pass to circos.lines.

pt.col

If type is "o", points color.

cex

If type is "o", points size.

pch

If type is "o", points type.

factors

The same as sectors. It will be removed in future versions.

Value

Object ccTrackGeom

Examples

NULL

Add points on all sections of a single track.

Description

Object ccTrackGeom will call the function circlize::circos.trackPoints while drawing.

Usage

ccTrackPoints(
  sectors,
  x,
  y,
  pch = par("pch"),
  col = par("col"),
  cex = par("cex"),
  bg = par("bg"),
  factors = sectors
)

Arguments

sectors

A factor or a character vector which represents the categories of data

x

Data points on x-axis

y

Data points on y-axis

pch

Point type

col

Point color

cex

Point size

bg

backgrond color

factors

The same as sectors. It will be removed in future versions.

Value

Object ccTrackGeom

Examples

NULL

Add texts on all sections of a single track.

Description

Object ccTrackGeom will call the function circlize::circos.trackText while drawing.

Usage

ccTrackText(
  sectors,
  x,
  y,
  labels,
  direction = NULL,
  facing = c("inside", "outside", "reverse.clockwise", "clockwise", "downward",
    "bending", "bending.inside", "bending.outside"),
  niceFacing = FALSE,
  adj = par("adj"),
  cex = 1,
  col = par("col"),
  font = par("font"),
  factors = sectors
)

Arguments

sectors

A factor or a character vector which represents the categories of data

x

Data points on x-axis

y

Data points on y-axis

labels

Labels

direction

deprecated, use facing instead.

facing

Facing of text

niceFacing

Should the facing of text be adjusted to fit human eyes?

adj

Adjustment for text

cex

Font size

col

Font color

font

Font style

factors

The same as sectors. It will be removed in future versions.

Value

Object ccTrackGeom

Examples

NULL

Draw violin plots

Description

Object ccCellGeom will call the function circlize::circos.violin while drawing.

Usage

ccViolin(
  value,
  pos,
  violin_width = 0.8,
  col = NA,
  border = "black",
  lwd = par("lwd"),
  lty = par("lty"),
  show_quantile = TRUE,
  pt.col = par("col"),
  cex = par("cex"),
  pch = 16,
  max_density = NULL
)

Arguments

value

A numeric vector, a matrix or a list. If it is a matrix, boxplots are made by columns.

pos

Positions of the boxes.

violin_width

Width of violins.

col

Filled color of boxes.

border

Color for the border as well as the quantile lines.

lwd

Line width.

lty

Line style

show_quantile

Whether to show the quantile lines.

pt.col

Point color

cex

Point size.

pch

Point type.

max_density

The maximal density value across several violins. It is used to compare between violins.

Value

Object ccCellGeom

Examples


library(circlizePlus)
cc <- ccPlot(sectors = letters[1:4], xlim = c(0, 10))
track <- ccTrack(ylim = c(0, 1))
cell <- ccCell(sector.index = "a") + ccViolin(value = replicate(runif(10),
n = 10, simplify = FALSE), pos = 1:10 - 0.5, col = 1:10)
track <- track + cell
cc + track

Draw x-axis

Description

Object ccCellGeom will call the function circlize::circos.axis while drawing.

Usage

ccXaxis(
  h = "top",
  major.at = NULL,
  labels = TRUE,
  major.tick = TRUE,
  labels.font = par("font"),
  labels.cex = par("cex"),
  labels.facing = "inside",
  labels.direction = NULL,
  labels.niceFacing = TRUE,
  direction = c("outside", "inside"),
  minor.ticks = 4,
  major.tick.length = NULL,
  lwd = par("lwd"),
  col = par("col"),
  labels.col = par("col"),
  labels.pos.adjust = TRUE
)

Arguments

h

Position of the x-axis, can be "top", "bottom" or a numeric value

major.at

If it is numeric vector, it identifies the positions of the major ticks. It can exceed xlim value and the exceeding part would be trimmed automatically. If it is NULL, about every 10 degrees there is a major tick.

labels

labels of the major ticks. Also, the exceeding part would be trimmed automatically. The value can also be logical (either an atomic value or a vector) which represents which labels to show.

major.tick

Whether to draw major tick. If it is set to FALSE, there will be no minor ticks neither.

labels.font

Font style for the axis labels.

labels.cex

Font size for the axis labels.

labels.facing

Facing of labels on axis, passing to circos.text

labels.direction

Deprecated, use facing instead.

labels.niceFacing

Should facing of axis labels be human-easy.

direction

Whether the axis ticks point to the outside or inside of the circle.

minor.ticks

Number of minor ticks between two close major ticks.

major.tick.length

Length of the major ticks, measured in "current" data coordinate. convert_y can be used to convert an absolute unit to the data coordinate.

lwd

Line width for ticks.

col

Color for the axes.

labels.col

Color for the labels.

labels.pos.adjust

Whether to adjust the positions of the first label and the last label so that the first label align to its left and the last label align to its right if they exceed the range on axes. The value can be a vector of length two which correspond to the first label and the last label.

Value

Object ccCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(sectors = letters[1:8], xlim = c(0, 1))
track <- ccTrack(ylim = c(0, 10))
cell <- ccCell(sector.index = "a") + ccXaxis()
track <- track + cell
cc + track

Draw y-axis

Description

Object ccCellGeom will call the function circlize::circos.yaxis while drawing.

Usage

ccYaxis(
  side = c("left", "right"),
  at = NULL,
  labels = TRUE,
  tick = TRUE,
  labels.font = par("font"),
  labels.cex = par("cex"),
  labels.niceFacing = TRUE,
  lwd = par("lwd"),
  col = par("col"),
  labels.col = par("col")
)

Arguments

side

add the y-axis on the left or right of the cell

at

If it is numeric vector, it identifies the positions of the ticks. It can exceed ylim value and the exceeding part would be trimmed automatically.

labels

labels of the ticks. The exceeding part would be trimmed automatically. The value can also be logical (either an atomic value or a vector) which represents which labels to show.

tick

Whether to draw ticks.

labels.font

font style for the axis labels

labels.cex

font size for the axis labels

labels.niceFacing

Should facing of axis labels be human-easy

lwd

line width for ticks

col

color for the axes

labels.col

color for the labels

Value

Object ccCellGeom

Examples

library(circlizePlus)
cc <- ccPlot(sectors = letters[1:8], xlim = c(0, 1))
track <- ccTrack(ylim = c(0, 10))
cell <- ccCell(sector.index = "a") + ccYaxis(side = "left")
track <- track + cell
cc + track

Data set in circlizePlus

Description

Example can be found in "4.2 Example 2: comparison of two pieces of code that use circlizePlus and circlize to implement the same requirements, respectively"

allele_frequency: A dataframe with 25,000 rows and 4 columns
copy_number: A dataframe with 24,788 rows and 5 columns
junctions: A dataframe with 2414 rows and 28 columns
r1: A dataframe with 2414 rows and 3 columns
r2: A dataframe with 2414 rows and 3 columns

Usage

data(example2)

data(example2)

data(example2)

data(example2)

data(example2)

Format

An object of class data.frame with 25000 rows and 4 columns.

An object of class data.frame with 24788 rows and 5 columns.

An object of class data.frame with 2414 rows and 28 columns.

An object of class data.frame with 2414 rows and 3 columns.

An object of class data.frame with 2414 rows and 3 columns.

Source

https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2025.1535368/full#h5

Examples


data(example2)
allele_frequency
copy_number
junctions
r1
r2

Draw the figures described by ccHeatmap

Description

Draw the figures described by ccHeatmap

Usage

## S4 method for signature 'ccHeatmap'
show(object)

Arguments

object

Object of ccHeatmap

Value

No return information

Examples


library(circlizePlus)
set.seed(123)
mat1 <- rbind(
  cbind(
    matrix(rnorm(50 * 5, mean = 1), nr = 50),
    matrix(rnorm(50 * 5, mean = -1), nr = 50)
  ),
  cbind(
    matrix(rnorm(50 * 5, mean = -1), nr = 50),
    matrix(rnorm(50 * 5, mean = 1), nr = 50)
  )
)
rownames(mat1) <- paste0("R", 1:100)
colnames(mat1) <- paste0("C", 1:10)
mat1 <- mat1[sample(100, 100), ] # randomly permute rows
split <- sample(letters[1:5], 100, replace = TRUE)
split <- factor(split, levels = letters[1:5])
col_fun1 <- colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))
show(ccHeatmap(mat = mat1, split = split, col = col_fun1))

Draw the figures described by ccPlot

Description

Draw the figures described by ccPlot

Usage

## S4 method for signature 'ccPlot'
show(object)

Arguments

object

Object of ccPlot

Value

No return information

Examples

library(circlizePlus)
n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),
                x = rnorm(n), y = runif(n))
library(circlizePlus)
par1=ccPar("track.height" = 0.1)
cc=ccPlot(sectors = df$sectors, x = df$x) + par1
track1 = ccTrack(sectors = df$sectors, y = df$y,
                 panel.fun = function(x, y) {
                   circos.text(CELL_META$xcenter,
                               CELL_META$cell.ylim[2] + mm_y(5),
                               CELL_META$sector.index)
                   circos.axis(labels.cex = 0.6)
                 })
cc=cc+track1
show(cc)