### Example Usage of print.CELL_META

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/print.CELL_META.html

Demonstrates the output when the print.CELL_META method is called. Currently, there are no specific examples provided in the documentation.

```R
# There is no example
NULL

#>
NULL
```

--------------------------------

### Install circlize from GitHub

Source: https://github.com/jokergoo/circlize/blob/master/README.md

Install the development version of the circlize package directly from GitHub using the devtools package.

```r
devtools::install_github("jokergoo/circlize")
```

--------------------------------

### Install circlize Package

Source: https://github.com/jokergoo/circlize/blob/master/docs/index.html

Install the circlize package from CRAN or directly from GitHub using devtools.

```r
install.packages("circlize")
```

```r
devtools::install_github("jokergoo/circlize")
```

--------------------------------

### Install circlize from CRAN

Source: https://github.com/jokergoo/circlize/blob/master/README.md

Install the circlize package from the Comprehensive R Archive Network (CRAN).

```r
install.packages("circlize")
```

--------------------------------

### Basic circos.axis setup

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.axis.html

Initializes a circos plot with sectors and then draws a basic x-axis on sector 'a'.

```R
sectors = letters[1:8]
circos.par(points.overflow.warning = FALSE)
circos.initialize(sectors, xlim = c(0, 10))

circos.trackPlotRegion(sectors, ylim = c(0, 10), track.height = 0.1,
    bg.border = NA, panel.fun = function(x, y) {
        circos.text(5, 10, get.cell.meta.data("sector.index"))
})

circos.trackPlotRegion(sectors, ylim = c(0, 10))

circos.axis(sector.index = "a")
```

--------------------------------

### Initialize Circos and Generate Genomic Rainfall Plot

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicRainfall.html

This example demonstrates how to initialize the circos plot with ideogram data and then generate a genomic rainfall plot using a list of bed-formatted data. It also includes adding genomic density tracks for comparison. Ensure the 'circlize' package and its example data are loaded.

```R
library(circlize)

# Load example data
load(system.file(package = "circlize", "extdata", "DMR.RData"))

# Initialize circos with ideogram
circos.initializeWithIdeogram(plotType = c("axis", "labels"))

# Define bed data as a list
bed_list <- list(DMR_hyper, DMR_hypo)

# Generate genomic rainfall plot
circos.genomicRainfall(bed_list, pch = 16, cex = 0.4, col = c("#FF000080", "#0000FF80"))

# Add genomic density tracks
circos.genomicDensity(bed_list[[1]], col = c("#FF000080"), track.height = 0.1)
circos.genomicDensity(bed_list[[2]], col = c("#0000FF80"), track.height = 0.1)

# Clear the circos plot
circos.clear()
```

--------------------------------

### Draw Arrows with Reversed Arrow Position

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.arrow.html

Example showing how to draw arrows with the arrow head at the 'start' position, effectively reversing the arrow's direction. This is controlled by the 'arrow.position' argument.

```R
circos.initialize(letters[1:4], xlim = c(0, 1))

tail = c("point", "normal", "point", "normal")
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    circos.arrow(x1 = 0, x2 = 1, y = 0.5, width = 0.4,
        arrow.head.width = 0.6, arrow.head.length = cm_x(1),
        col = col[CELL_META$sector.numeric.index],
        tail = tail[CELL_META$sector.numeric.index],
        arrow.position = "start")
}, bg.border = NA, track.height = 0.4)
```

--------------------------------

### get.all.sector.index

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Get index for all sectors.

```APIDOC
## get.all.sector.index()

### Description
Get index for all sectors.

### Method
Not specified (likely a function call in an R package)

### Endpoint
Not applicable (function call)

### Parameters
None specified in the source.

### Request Example
```r
get.all.sector.index()
```

### Response
None specified in the source.
```

--------------------------------

### Example: Update and draw a rectangle in a specific cell

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.updatePlotRegion.html

This example demonstrates initializing a Circos plot, adding a track with text, then updating a specific cell ('b', track 1) and drawing a semi-transparent red rectangle within it.

```r
circos.initialize(letters[1:8], xlim = c(0, 1))

circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    circos.text(CELL_META$xcenter, CELL_META$ycenter, CELL_META$sector.index)
})

circos.update(sector.index = "b", track.index = 1)

circos.rect(CELL_META$cell.xlim[1], CELL_META$cell.ylim[1],
            CELL_META$cell.xlim[2], CELL_META$cell.ylim[2],
            col = "#FF000080")

circos.clear()
```

--------------------------------

### Initialize sectors and tracks, then convert coordinates

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circlize.html

This example demonstrates initializing sectors and tracks using `circos.initialize` and `circos.track`, followed by converting a specific data point (x=0.5, y=0.5) to polar coordinates using `circlize`. It also shows how to clear the circos plot afterwards.

```R
pdf(NULL)
sectors = c("a", "b")
circos.initialize(sectors, xlim = c(0, 1))
circos.track(ylim = c(0, 1))
# x = 0.5, y = 0.5 in sector a and track 1
circlize(0.5, 0.5, sector.index = "a", track.index = 1)

circos.clear()
dev.off()
```

--------------------------------

### Setting start.degree

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.par.html

Configures the starting degree from which the circle drawing begins. The degree is measured in the standard polar coordinate system, which is counter-clockwise.

```R
circos.par(start.degree = 90)
```

--------------------------------

### get.current.sector.index

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Get current sector index.

```APIDOC
## get.current.sector.index()

### Description
Get current sector index.

### Method
Not specified (likely a function call in an R package)

### Endpoint
Not applicable (function call)

### Parameters
None specified in the source.

### Request Example
```r
get.current.sector.index()
```

### Response
None specified in the source.
```

--------------------------------

### Add points to a stacked track with dynamic size and color

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicPoints.html

This example adds points to a stacked genomic track, with point size and color dynamically mapped from the data. It also draws reference lines.

```R
circos.genomicTrack(bed_list, stack = TRUE,
    panel.fun = function(region, value, ...) {
    cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
    i = getI(...)
    circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})
```

--------------------------------

### circos.par()

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Sets or gets parameters for the circular layout.

```APIDOC
## circos.par()

### Description
Parameters for the circular layout.

### Method
N/A (R function)

### Endpoint
N/A (R function)

### Parameters
N/A (R function)

### Request Example
N/A (R function)

### Response
N/A (R function)
```

--------------------------------

### get.current.track.index

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Get current track index.

```APIDOC
## get.current.track.index()

### Description
Get current track index.

### Method
Not specified (likely a function call in an R package)

### Endpoint
Not applicable (function call)

### Parameters
None specified in the source.

### Request Example
```r
get.current.track.index()
```

### Response
None specified in the source.
```

--------------------------------

### Basic Violin Plot Example

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.violin.html

Initializes a circos plot and draws multiple violin plots with default settings within a track. This is useful for visualizing distributions at different positions.

```R
circos.initialize(letters[1:4], xlim = c(0, 10))

circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    for(pos in seq(0.5, 9.5, by = 1)) {
        value = runif(10)
        circos.violin(value, pos)
    }
})

circos.clear()
```

--------------------------------

### Plotting Genomic Points with Scaled Size and Color

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicPoints.html

This example demonstrates plotting genomic points where the size (cex) and color are dynamically determined by the data values. It also adds a horizontal line for context using circos.lines.

```R
[circos.genomicTrack](circos.genomicTrack.html)(bed, stack = TRUE, panel.fun = function(region, value, ...) {
    cex = (value[[1]] - [min](https://rdrr.io/r/base/Extremes.html)(value[[1]]))/([max](https://rdrr.io/r/base/Extremes.html)(value[[1]]) - [min](https://rdrr.io/r/base/Extremes.html)(value[[1]]))
    i = [getI](getI.html)(...)
    circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
    cell.xlim = [get.cell.meta.data](get.cell.meta.data.html)("cell.xlim")
    [circos.lines](circos.lines.html)(cell.xlim, [c](https://rdrr.io/r/base/c.html)(i, i), lty = 2, col = "#00000040")
})
```

--------------------------------

### Initialize with Human Species (hg18)

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.initializeWithIdeogram.html

Initializes the circular plot by automatically downloading cytoband data for a specified species, using 'hg18' as an example for human.

```R
circos.initializeWithIdeogram(species = "hg18")
```

--------------------------------

### Add specific points with custom styling

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.points.html

Adds points to a specific sector and track with custom point shape and color. This example shows how to target a particular cell and override default graphical parameters.

```r
circos.points(runif(10), runif(10), sector.index = "c", pch = 16, col = "red")
```

--------------------------------

### Add points to a stacked genomic track

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicPoints.html

This example shows how to add points to a stacked genomic track. It includes drawing dashed lines for visual reference within each cell.

```R
circos.genomicTrack(bed, stack = TRUE, panel.fun = function(region, value, ...) {
    circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
    i = getI(...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})
```

--------------------------------

### Draw Genomic Rectangles with Specified Y-positions

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicRect.html

This example shows how to draw genomic rectangles with explicitly defined top and bottom y-positions using the ytop and ybottom arguments. It also adds dashed lines to each cell, indicating the cell's y-position.

```R
circos.genomicTrack(bed_list, ylim = c(0, 3),
    panel.fun = function(region, value, ...) {
    i = getI(...)
    circos.genomicRect(region, value, ytop = i+0.4, ybottom = i-0.4, col = f(value[[1]]),
        border = NA, ...)

cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#000000")
})
```

--------------------------------

### Draw Genomic Rectangles with Color Mapping

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicRect.html

This example demonstrates drawing genomic rectangles using circos.genomicRect. It maps values from the input data to colors using a colorRamp2 function. It also adds dashed lines to each cell, indicating the cell's y-position.

```R
circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.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"))
circos.genomicTrack(bed_list, stack = TRUE,
    panel.fun = function(region, value, ...) {

circos.genomicRect(region, value, col = f(value[[1]]), 
        border = NA, ...)
    i = getI(...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#000000")
})
```

--------------------------------

### getI

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Which data that `panel.fun` is using.

```APIDOC
## getI()

### Description
Which data that `panel.fun` is using.

### Method
Not specified (likely a function call in an R package)

### Endpoint
Not applicable (function call)

### Parameters
None specified in the source.

### Request Example
```r
getI()
```

### Response
None specified in the source.
```

--------------------------------

### Initialize with tick labels starting from non-zero

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicInitialize.html

Initializes a circular plot with a custom data frame, disabling tick labels from starting at zero.

```R
circos.clear()
circos.genomicInitialize(df, tickLabelsStartFromZero = FALSE)
```

--------------------------------

### circos.initializeWithIdeogram()

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Initializes the circular layout using an ideogram.

```APIDOC
## circos.initializeWithIdeogram()

### Description
Initialize the circular layout with an ideogram.

### Method
N/A (R function)

### Endpoint
N/A (R function)

### Parameters
N/A (R function)

### Request Example
N/A (R function)

### Response
N/A (R function)
```

--------------------------------

### circos.heatmap.initialize()

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Initializes circular heatmaps.

```APIDOC
## circos.heatmap.initialize()

### Description
Initialize circular heatmaps.

### Method
N/A (R function)

### Endpoint
N/A (R function)

### Parameters
N/A (R function)

### Request Example
N/A (R function)

### Response
N/A (R function)
```

--------------------------------

### Real-time Clock with Circos Axis

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.axis.html

Demonstrates how to create a real-time clock visualization using circos.axis. Requires initialization of circos plot and sectors. The loop updates clock hands every second.

```R
if(FALSE) {

############### real-time clock #################
factors = letters[1]

circos.par("gap.degree" = 0, "cell.padding" = c(0, 0, 0, 0), "start.degree" = 90)
circos.initialize(sectors, xlim = c(0, 12))
circos.trackPlotRegion(sectors, ylim = c(0, 1), bg.border = NA)
circos.axis(sector.index = "a", major.at = 0:12, labels = "",
    direction = "inside", major.tick.length = mm_y(3))
circos.text(1:12, rep(0.5, 12), 1:12, facing = "downward")

while(1) {
    current.time = as.POSIXlt(Sys.time())
    sec = ceiling(current.time$sec)
    min = current.time$min
    hour = current.time$hour

# erase the clock hands
    draw.sector(rou1 = 0.8, border = "white", col = "white")

sec.degree = 90 - sec/60 * 360
    arrows(0, 0, cos(sec.degree/180*pi)*0.8, sin(sec.degree/180*pi)*0.8)

min.degree = 90 - min/60 * 360
    arrows(0, 0, cos(min.degree/180*pi)*0.7, sin(min.degree/180*pi)*0.7, lwd = 2)

hour.degree = 90 - hour/12 * 360 - min/60 * 360/12
    arrows(0, 0, cos(hour.degree/180*pi)*0.4, sin(hour.degree/180*pi)*0.4, lwd = 2)

Sys.sleep(1)
}
circos.clear()
}
```

--------------------------------

### circos.heatmap.initialize

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.heatmap.initialize.html

Initializes circular heatmaps by setting up the necessary structures and parameters based on the input matrix and optional configurations.

```APIDOC
## circos.heatmap.initialize

### Description
Initializes circular heatmaps.

### Function Signature
`circos.heatmap.initialize(mat, split = NULL, cluster = TRUE, clustering.method = "complete", distance.method = "euclidean", dend.callback = function(dend, m, si) reorder(dend, rowMeans(m)))

### Arguments

*   **mat** (matrix or vector) - The input data matrix or vector. If a vector, it is transformed into a one-column matrix.
*   **split** (categorical variable, optional) - Used to split the matrix into a list of matrices.
*   **cluster** (boolean, optional) - Whether to apply clustering on rows. Defaults to TRUE.
*   **clustering.method** (string, optional) - The clustering method to use, passed to `hclust`. Defaults to "complete".
*   **distance.method** (string, optional) - The distance method to use, passed to `dist`. Defaults to "euclidean".
*   **dend.callback** (function, optional) - A callback function applied to the dendrogram in every sector. Defaults to a function that reorders the dendrogram based on row means.

### See Also
[https://jokergoo.github.io/2020/05/21/make-circular-heatmaps/](https://jokergoo.github.io/2020/05/21/make-circular-heatmaps/)
```

--------------------------------

### get.cell.meta.data

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Get the meta data of a cell.

```APIDOC
## get.cell.meta.data()

### Description
Get the meta data of a cell.

### Method
Not specified (likely a function call in an R package)

### Endpoint
Not applicable (function call)

### Parameters
None specified in the source.

### Request Example
```r
get.cell.meta.data()
```

### Response
None specified in the source.
```

--------------------------------

### Generate and display the first Chord diagram

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/calc_gap.html

This snippet demonstrates how to create and visualize a Chord diagram using `chordDiagram`. It sets directional flow, grid colors, transparency, and specific gap values.

```R
set.seed(123)
mat1 = matrix(sample(20, 25, replace = TRUE), 5)
chordDiagram(mat1, directional = 1, grid.col = rep(1:5, 2), transparency = 0.5,
    big.gap = 10, small.gap = 1)
```

--------------------------------

### Initialize with default settings

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicInitialize.html

Initializes a circular plot using genomic data from a cytoband data frame with default settings.

```R
df = read.cytoband()$df
circos.genomicInitialize(df)
```

--------------------------------

### circos.polygon

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.polygon.html

Draws a polygon on the circos plot. The start and end points of the polygon should overlap.

```APIDOC
## circos.polygon

### Description
Draws a polygon on the circos plot. The start and end points of the polygon should overlap.

### Function Signature
`circos.polygon(x, y, sector.index = get.current.sector.index(), track.index = get.current.track.index(), ...)`

### Arguments
- **x** (numeric vector): Data points on the x-axis.
- **y** (numeric vector): Data points on the y-axis.
- **sector.index** (character or numeric): Index for the sector where the polygon will be drawn. Defaults to the current sector.
- **track.index** (numeric): Index for the track where the polygon will be drawn. Defaults to the current track.
- **...**: Additional arguments passed to the `polygon` function.

### Details
This function is similar to the base R `polygon` function. Ensure that the start point of the polygon data overlaps with the end point for proper rendering.
```

--------------------------------

### Get Current Sector Index

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/get.current.sector.index.html

Retrieves the name of the current sector. This function does not take any arguments.

```APIDOC
## get.current.sector.index()

### Description
Retrieves the name of the current sector.

### Method
Function Call

### Parameters
This function does not take any parameters.

### Response
#### Success Response
- **sector_name** (string) - The name of the current sector.

### Response Example
```json
"sector_name"
```
```

--------------------------------

### Initialize with Cytoband File

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.initializeWithIdeogram.html

Initializes the circular plot using a specified cytoband file. Ensure the file path is correct.

```R
cytoband.file <- system.file(package = "circlize", "extdata", "cytoBand.txt")
circos.initializeWithIdeogram(cytoband.file)
```

--------------------------------

### Default Initialization

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.initializeWithIdeogram.html

Initializes the Circos plot with default settings.

```APIDOC
## Default Initialization

### Description
Initializes the Circos plot with default settings.

### Method
`circos.initializeWithIdeogram()`

### Parameters
None

### Request Example
```R
circos.initializeWithIdeogram()
```

### Response
None (modifies the Circos plotting state)
```

--------------------------------

### Clear Circos Plot

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.barplot.html

Clears the current circos plot. This should be called after drawing is complete or before starting a new plot.

```R
circos.clear()
```

--------------------------------

### cm_h

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/cm_h.html

Converts units, specifically height, within the circlize package. For detailed usage and examples, refer to the convert_length documentation.

```APIDOC
## cm_h(h)

### Description
Converts units, specifically height.

### Arguments
#### h
- **h** (numeric) - The height in numeric.

### Details
See explanations in `[convert_length](convert_length.html)` page.

### Examples

```r
# see examples in `convert_length` page
NULL
```
```

--------------------------------

### Create a Matrix for Chord Diagram

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/chordDiagram.html

Generates a sample matrix with specified dimensions and labels, suitable for input into the chordDiagram function. Ensure row and column names are set appropriately for your data.

```R
set.seed(999)
mat = matrix(sample(18, 18), 3, 6)
rownames(mat) = paste0("S", 1:3)
colnames(mat) = paste0("E", 1:6)
```

--------------------------------

### Initialize Circos and Add Points

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.trackPoints.html

Initializes a circos plot with 8 sectors and sets the x-axis limits. Then, it creates a data frame with random sectors, x, and y values. A track is added with y-axis limits, and finally, points are added to the track using circos.trackPoints with specified point type and color based on a factor.

```R
circos.initialize(letters[1:8], xlim = c(0, 1))

df = data.frame(sectors = sample(letters[1:8], 100, replace = TRUE),
                x = runif(100), y = runif(100))
circos.track(ylim = c(0, 1))

circos.trackPoints(df$sectors, x = df$x, y = df$y, pch = 16, col = as.numeric(factor(df$fa)))

circos.clear()
```

--------------------------------

### Initialize with Default Cytoband

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.initializeWithIdeogram.html

Initializes the circular plot using the default cytoband data. This is a basic setup for a human genome ideogram.

```R
circos.initializeWithIdeogram()
```

--------------------------------

### Initialize with custom data frame

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicInitialize.html

Initializes a circular plot using a custom data frame with gene names, start, and end positions.

```R
df = data.frame(name = c("TP53", "TP63", "TP73"),
                start = c(7565097, 189349205, 3569084),
                end = c(7590856, 189615068, 3652765),
                stringsAsFactors = FALSE)
circos.genomicInitialize(df)
```

--------------------------------

### Get meta data names

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/names.CELL_META.html

Use this function to retrieve all available meta data names for the current cell. It is an S3 method for CELL_META.

```R
names(CELL_META)
```

--------------------------------

### Initialize and Configure Tracks with Different Height Units

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/convert_length.html

Demonstrates how to initialize a circular plot and add tracks with heights defined in millimeters, centimeters, and inches. This showcases the flexibility in specifying track dimensions using various units.

```R
sectors = letters[1:10]
circos.par(cell.padding = c(0, 0, 0, 0), track.margin = c(0, 0))
circcos.initialize(sectors, xlim = cbind(rep(0, 10), runif(10, 0.5, 1.5)))

circcos.track(ylim = c(0, 1), track.height = mm_h(5))

circcos.par(track.margin = c(0, mm_h(2)))
circcos.track(ylim = c(0, 1), track.height = cm_h(1))

circcos.par(track.margin = c(0, mm_h(5)))
circcos.track(ylim = c(0, 1), track.height = inch_h(1))

circcos.clear()
```

--------------------------------

### Draw Boxplots with Custom Colors

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.boxplot.html

Demonstrates drawing multiple boxplots with distinct colors assigned to each. This example uses replicated random data for each boxplot.

```R
circos.initialize(letters[1:4], xlim = c(0, 10))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    value = replicate(runif(10), n = 10, simplify = FALSE)
    circos.boxplot(value, 1:10 - 0.5, col = 1:10)
})
circos.clear()
```

--------------------------------

### circos.initialize Function

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.initialize.html

Initializes the circular layout by defining sectors and their properties. This function prepares the plotting area for creating circular visualizations.

```APIDOC
## circos.initialize

### Description
Initializes the circular layout.

### Arguments
*   **sectors** (factor or character vector) - Represents data categories for sectors.
*   **x** (vector) - Data on x-axes.
*   **xlim** (vector or matrix) - Ranges for values on x-axes.
*   **sector.width** (vector) - Width for each sector. Can be a single value for all sectors or a vector with lengths equal to the number of sectors.
*   **factors** (factor or character vector) - Alias for `sectors`. Will be removed in future versions.

### Details
The function allocates sectors based on x-axis values or `xlim`. Sector positions are calculated based on x-axis values or `xlim`. If `x` is provided, its length must match `factors`. If `xlim` is a matrix, row names should cover all sector names for automatic adjustment. Sector widths can be manually set but it's generally recommended to let the function calculate them based on data ranges.

### See Also
[https://jokergoo.github.io/circlize_book/book/circular-layout.html](https://jokergoo.github.io/circlize_book/book/circular-layout.html)
```

--------------------------------

### get.cell.meta.data

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/get.cell.meta.data.html

Retrieves metadata for a specified cell. This function is useful within `panel.fun` to get detailed information about the current cell being rendered in a circular layout.

```APIDOC
## get.cell.meta.data

### Description
Get the meta data of a cell.

### Method
`get.cell.meta.data(name, sector.index = get.current.sector.index(), track.index = get.current.track.index())
`

### Arguments
* **name** - The name of the meta information to retrieve. Only one name is supported at a time.
* **sector.index** - (Optional) The index of the sector. Defaults to the current sector index.
* **track.index** - (Optional) The index of the track. Defaults to the current track index.

### Details
The following meta information for a cell can be obtained:
* `sector.index`: The name (index) for the sector
* `sector.numeric.index`: Numeric index for the sector
* `track.index`: Numeric index for the track
* `xlim`: Minimal and maximal values on the x-axis
* `ylim`: Minimal and maximal values on the y-axis
* `xrange`: Range of `xlim`. It equals to `xlim[2] - xlim[1]`
* `yrange`: Range of `ylim`
* `xcenter`: Center of x-axis. It equals to `(xlim[2] + xlim[1])/2`
* `ycenter`: Center of y-axis
* `cell.xlim`: Minimal and maximal values on the x-axis extended by cell paddings
* `cell.ylim`: Minimal and maximal values on the y-axis extended by cell paddings
* `xplot`: Degrees for right and left borders of the cell. The values ignore the direction of the circular layout.
* `yplot`: Radius for top and bottom borders of the cell.
* `cell.width`: Width of the cell, in degrees.
* `cell.height`: Height of the cell, simply `yplot[2] - yplot[1]`
* `cell.start.degree`: Same as `xplot[1]`
* `cell.end.degree`: Same as `xplot[2]`
* `cell.bottom.radius`: Same as `yplot[1]`
* `cell.top.radius`: Same as `yplot[2]`
* `track.margin`: Margin for the cell
* `cell.padding`: Padding for the cell

### Example
```r
# Initialize circos
sectors = letters[1:4]
circo.initialize(sectors, xlim = c(0, 1))

# Plot a track and print xlim for each cell
circos.trackPlotRegion(ylim = c(0, 1), panel.fun = function(x, y) {
    print(get.cell.meta.data("xlim"))
})

# Get specific meta data
print(get.cell.meta.data("xlim", sector.index = "a", track.index = 1))

# Clear circos
circo.clear()
```
```

--------------------------------

### Add points to a genomic track

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicPoints.html

This snippet demonstrates how to add points to a genomic track using circos.genomicPoints. It requires prior setup with circos.par and circos.initializeWithIdeogram.

```R
circos.par("track.height" = 0.1)
circos.initializeWithIdeogram(plotType = NULL)

bed = generateRandomBed(nr = 100)
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
    circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
```

--------------------------------

### highlight.sector

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Highlight sectors and tracks.

```APIDOC
## highlight.sector()

### Description
Highlight sectors and tracks.

### Method
Not specified (likely a function call in an R package)

### Endpoint
Not applicable (function call)

### Parameters
None specified in the source.

### Request Example
```r
highlight.sector()
```

### Response
None specified in the source.
```

--------------------------------

### Get X-axis Limits for Current Cell

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/get.cell.meta.data.html

Demonstrates how to retrieve the x-axis limits of the current cell within a track. This is useful for understanding the plotting boundaries for the active cell.

```R
sectors <- letters[1:4]
circos.initialize(sectors, xlim = c(0, 1))
circos.trackPlotRegion(ylim = c(0, 1), panel.fun = function(x, y) {
    print(get.cell.meta.data("xlim"))
})
```

--------------------------------

### circos.genomicInitialize()

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Initializes a circular plot with any genomic data.

```APIDOC
## circos.genomicInitialize()

### Description
Initialize circular plot with any genomic data.

### Method
N/A (R function)

### Endpoint
N/A (R function)

### Parameters
N/A (R function)

### Request Example
N/A (R function)

### Response
N/A (R function)
```

--------------------------------

### Initialize Circos with Ideogram and Add Genomic Axis

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicAxis.html

Initializes a circos plot with an ideogram and adds a genomic axis to the top of the plot. This is a common setup for genomic visualizations.

```R
circos.initializeWithIdeogram(chromosome.index = paste0("chr", 1:4), plotType = NULL)
circos.track(ylim = c(0, 1), panel.fun = function(x, y) circos.genomicAxis())
```

--------------------------------

### Initialize with Mouse Species (mm10)

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.initializeWithIdeogram.html

Initializes the circular plot by automatically downloading cytoband data for a specified species, using 'mm10' for mouse.

```R
circos.initializeWithIdeogram(species = "mm10")
```

--------------------------------

### Get X-axis Limits for a Specific Cell

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/get.cell.meta.data.html

Shows how to retrieve the x-axis limits for a specific cell identified by its sector and track index. This allows targeted data retrieval for non-current cells.

```R
print(get.cell.meta.data("xlim", sector.index = "a", track.index = 1))
```

--------------------------------

### show.index

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/index.html

Label the sector index and the track index on each cell.

```APIDOC
## show.index()

### Description
Label the sector index and the track index on each cell.

### Method
Not specified (likely a function call in an R package)

### Endpoint
Not applicable (function call)

### Parameters
None specified in the source.

### Request Example
```r
show.index()
```

### Response
None specified in the source.
```

--------------------------------

### Basic Sector Drawing

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/draw.sector.html

Draws a basic sector with default parameters. Requires a plot to be initialized.

```R
plot(c(-1, 1), c(-1, 1), type = "n", axes = FALSE, ann = FALSE, asp = 1)

draw.sector(20, 0)
```

--------------------------------

### Draw segments between points

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.segments.html

This example demonstrates how to draw multiple segments within a circos plot. It initializes the circos plot, defines a track, and then uses circos.segments to draw horizontal and vertical lines.

```R
circos.initialize(letters[1:8], xlim = c(0, 1))
circos.track(ylim = c(0, 1), track.height = 0.3, panel.fun = function(x, y) {
    x = seq(0.2, 0.8, by = 0.2)
    y = seq(0.2, 0.8, by = 0.2)

circos.segments(x, 0.1, x, 0.9)
    circos.segments(0.1, y, 0.9, y)
})

circos.clear()
```

--------------------------------

### Draw Genomic Rectangles with Color as Index

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicRect.html

This example draws genomic rectangles where the color of each rectangle is determined by its index within the track. This provides a simple way to differentiate adjacent rectangles visually.

```R
circos.genomicTrack(bed_list, panel.fun = function(region, value, ...) {
    i = getI(...)
    circos.genomicRect(region, value, col = i, border = NA, ...)

})
```

--------------------------------

### Draw Arrows with Different Tail Shapes

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.arrow.html

Example demonstrating how to draw arrows with different tail shapes ('point' and 'normal') within a circos track. The arrow position is set to 'end' by default.

```R
op = par(no.readonly = TRUE)
par(mfrow = c(1, 2))
circos.initialize(letters[1:4], xlim = c(0, 1))
col = rand_color(4)
tail = c("point", "normal", "point", "normal")
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    circos.arrow(x1 = 0, x2 = 1, y = 0.5, width = 0.4,
        arrow.head.width = 0.6, arrow.head.length = cm_x(1),
        col = col[CELL_META$sector.numeric.index],
        tail = tail[CELL_META$sector.numeric.index])
}, bg.border = NA, track.height = 0.4)
circos.clear()
```

--------------------------------

### Initialize and Highlight Sectors

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/highlight.sector.html

Initializes a circular plot with sectors and then highlights specific sectors with different colors and borders. This is useful for visually distinguishing parts of the circular plot.

```R
sectors 
<- letters[1:8]
circos.initialize(sectors, xlim = c(0, 1))

for(i in 1:4) {
    circos.trackPlotRegion(ylim = c(0, 1))
}

circos.info(plot = TRUE)

highlight.sector(c("a", "h"), track.index = 1)

highlight.sector("c", col = "#00FF0040")

highlight.sector("d", col = NA, border = "red", lwd = 2)

highlight.sector("e", col = "#0000FF40", track.index = c(2, 3))

highlight.sector(c("f", "g"), col = NA, border = "green",
    lwd = 2, track.index = c(2, 3))

highlight.sector(sectors, col = "#FFFF0040", track.index = 4)

circos.clear()
```

--------------------------------

### Create Chord Diagram from Matrix

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/chordDiagram.html

Generates a chord diagram directly from a numeric matrix. Ensure the matrix is properly formatted.

```R
df <- data.frame(from = rep(rownames(mat), times = ncol(mat)),
    to = rep(colnames(mat), each = nrow(mat)),
    value = as.vector(mat),
    stringsAsFactors = FALSE)

chordDiagram(mat)
```

--------------------------------

### Initialize with custom sector names

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.genomicInitialize.html

Initializes a circular plot with a custom data frame and provides custom names for each sector.

```R
circos.clear()
circos.genomicInitialize(df, sector.names = c("tp53", "tp63", "tp73"))
```

--------------------------------

### Apply color interpolation function

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/colorRamp2.html

Applies the generated color interpolation function to a vector of numeric values to get corresponding colors. Values outside the defined breaks will be assigned the color of the nearest break.

```R
col_fun(c(-2, -1, -0.5, 0, 0.5, 1, 2))
```

--------------------------------

### circos.initializeWithIdeogram

Source: https://github.com/jokergoo/circlize/blob/master/docs/reference/circos.initializeWithIdeogram.html

Initializes the circular plot with chromosome ideograms. It can take a path to a cytoband file, a species name to download data, or a pre-read data frame. It also allows customization of chromosome sorting and which components to plot.

```APIDOC
## circos.initializeWithIdeogram

### Description
Initializes the circular plot where each sector corresponds to a chromosome. It can use a cytoband file or download species-specific data. Options are available to control chromosome order, sorting, and what elements (ideogram, axis, labels) are drawn.

### Arguments

*   **cytoband** (path or data frame) - Path to the cytoband file or a data frame containing cytoband data. Defaults to hg19 cytoband.
*   **species** (string, optional) - Abbreviation for species (e.g., "hg19", "mm10"). If specified, downloads cytoband data from UCSC.
*   **sort.chr** (boolean) - Whether to sort chromosome names. Defaults to TRUE. If `chromosome.index` is set, this is enforced to FALSE.
*   **chromosome.index** (vector, optional) - A subset of chromosomes to use and to reorder chromosomes.
*   **major.by** (numeric, optional) - Increment for major ticks. Passed to `circos.genomicInitialize`.
*   **plotType** (vector of strings) - Which tracks to draw: "ideogram", "axis", "labels". Defaults to c("ideogram", "axis", "labels"). If no ideogram is available for the species, "ideogram" is excluded. If NULL, only initializes the plot without drawing.
*   **track.height** (numeric, optional) - Height of the track containing "axis" and "labels".
*   **ideogram.height** (numeric, optional) - Height of the ideogram track. Defaults to convert_height(2, "mm").
*   **...** - Additional arguments passed to `circos.genomicInitialize`.

### Details
This function prepares the circular plot for genomic data visualization. It handles the loading and ordering of chromosome information, passing the processed data to `circos.genomicInitialize`. Customization of the ideogram style is possible through user-defined code.

### See Also
[https://jokergoo.github.io/circlize_book/book/initialize-genomic-plot.html#initialize-cytoband](https://jokergoo.github.io/circlize_book/book/initialize-genomic-plot.html#initialize-cytoband)

### Examples

```R
# Initialize with default settings (hg19 cytoband)
circos.initializeWithIdeogram()

# Initialize using a local cytoband file
cytoband.file <- system.file(package = "circlize", "extdata", "cytoBand.txt")
circos.initializeWithIdeogram(cytoband.file)

# Initialize using a species name (e.g., human hg18)
circos.initializeWithIdeogram(species = "hg18")

# Initialize using a specific subset of chromosomes
circos.initializeWithIdeogram(chromosome.index = c("chr1", "chr2"))

# Initialize with custom chromosome order and no sorting
cytoband <- read.table(cytoband.file, sep = "\t", colClasses = c("character", "numeric", "numeric", "character", "character"))
circos.initializeWithIdeogram(cytoband, sort.chr = FALSE)

# Initialize with custom factor levels for chromosome order
cytoband[[1]] <- factor(cytoband[[1]], levels = paste0("chr", c(22:1, "X", "Y")))
circos.initializeWithIdeogram(cytoband, sort.chr = FALSE)
```
```