### Basic Track Visualization Example

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Demonstrates the fundamental usage of trackViewer for visualizing a single genomic track. This serves as a starting point for most use cases.

```R
library(trackViewer)

# Example: Visualize a BED file
file_path <- "path/to/your/data.bed"
track_data <- importScore(file_path)
viewTracks(trackList = list(track_data))
```

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

### Install trackViewer via BiocManager

Source: https://github.com/jianhong/trackviewer/blob/devel/README.md

Use this command to install the package from Bioconductor within an R session.

```r
library(BiocManager)
BiocManager::install("trackViewer")
```

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

### Create and modify a track from imported data

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Shows how to create a track object by importing data from a BED file, then modify its style and x-scale parameters. Includes an example of clearing the track's data.

```r
# Create a track from imported data
fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED")

# Modify track style
setTrackStyleParam(fox2, "color", c("red", "green"))
setTrackStyleParam(fox2, "tracktype", "peak")

# Set x-scale parameters
setTrackXscaleParam(fox2, "gp", list(cex=0.5))

# Clear data
fox2$dat <- GRanges(score=numeric(0))
```

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

### Track X-Scale Parameter Modification Example

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Demonstrates how to modify x-scale parameters for a track object using `setTrackXscaleParam`.

```APIDOC
## Modifying Track X-Scale Parameters

### Description
Use `setTrackXscaleParam` to adjust x-scale related parameters of a track.

### Method
`setTrackXscaleParam(track, attr, value)`

### Parameters
- **track** (track): The track object.
- **attr** (character): The x-scale attribute to change (e.g., "gp").
- **value** (list): The new value for the x-scale attribute.

### Example
```r
# Set x-scale parameters
setTrackXscaleParam(fox2, "gp", list(cex=0.5))
```
```

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

### ideogramPlot Parameter List Example

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

An example of a parameter list for ideogramPlot, demonstrating options for plot viewport, track heights, labels, and data display types. Configure this list to customize the appearance and data representation in ideogram plots.

```r
parameterList = list(
    vp = plotViewport(margins=c(.1, 4.1, .3, .1)),
    ideoHeight = unit(1/(1+n_datasets), "npc"),
    vgap = unit(.3, "lines"),
    ylabs = "auto",
    ylabsRot = 0,
    ylabsPos = unit(2.5, "lines"),
    xaxis = FALSE,
    yaxis = FALSE,
    xlab = "",
    types = "barplot",  # or "line", "point", "heatmap"
    heights = NULL,
    dataColumn = "score",
    gps = gpar(col="black", fill="gray")
)
```

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

### Track Style Modification Example

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Demonstrates how to modify the visual style of a track object using `setTrackStyleParam`.

```APIDOC
## Modifying Track Style

### Description
Use `setTrackStyleParam` to adjust visual attributes of a track.

### Method
`setTrackStyleParam(track, attr, value)`

### Parameters
- **track** (track): The track object to modify.
- **attr** (character): The style attribute to change (e.g., "color", "tracktype").
- **value** (any): The new value for the style attribute.

### Example
```r
# Create a track from imported data
fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED")

# Modify track style
setTrackStyleParam(fox2, "color", c("red", "green"))
setTrackStyleParam(fox2, "tracktype", "peak")
```
```

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

### Chromosome Navigation

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Provides examples of how to navigate between chromosomes or specific genomic locations. Functions like getLocation are useful for this purpose.

```R
library(trackViewer)

# Example: Navigate to a specific location
# Assuming a trackList is already defined
viewTracks(trackList = myTrackList, genome = "hg19", location = "chr1:100000-200000")

# Or using getLocation to get coordinates
coords <- getLocation(genome = "hg19", chr = "chr1", pos = 150000)
print(coords)
```

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

### Launch Interactive Track Browser

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/README.md

Create tracks as usual and then launch an interactive web browser session using browseTracks with specified dimensions.

```r
# Create tracks as before
tracks <- trackList(...)

# Launch interactive browser
browseTracks(tracks, gr=region, width=800, height=600)
```

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

### Initialize trackStyle Object

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

Constructs a new trackStyle object with default or specified parameters. Use this to define the visual appearance of a track.

```r
new("trackStyle",
    tracktype="peak",
    color=c("black", "black"),
    NAcolor="white",
    breaks=0,
    height=NA,
    marginTop=0,
    marginBottom=0.05,
    xscale=new("xscale"),
    yaxis=new("yaxisStyle"),
    ylim=NA,
    ylabpos="left",
    ylablas=0,
    ylabgp=list(),
    ysplit=0.5)

```

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

### Save Track Visualizations to Files (R)

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/common-patterns.md

Demonstrates saving track visualizations to PDF, PNG, SVG, and interactive HTML formats. Ensure necessary libraries are loaded.

```r
library(trackViewer)

track <- importScore("data.bw", format="BigWig")
gr <- GRanges("chr1", IRanges(1e6, 2e6))

# Save as PDF
pdf("tracks.pdf", width=10, height=6)
viewTracks(trackList(track), gr=gr)
dev.off()

# Save as PNG
png("tracks.png", width=800, height=400)
viewTracks(trackList(track), gr=gr)
dev.off()

# Save as SVG
svg("tracks.svg", width=10, height=6)
viewTracks(trackList(track), gr=gr)
dev.off()

# Interactive widget to HTML
library(htmlwidgets)
widget <- browseTracks(trackList(track), gr=gr)
saveWidget(widget, "tracks.html")
```

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

### Setting Xscale Graphics Parameters

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/types.md

Illustrates how to set graphical parameters for an xscale object, such as line color, width, text size, and font style.

```r
xscale$gp <- list(
    col="black",          # Line color
    lwd=1,               # Line width
    cex=1,               # Text size
    fontface="plain"     # Font style
)
```

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

### xscale

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Defines x-scale visualization on tracks, including start and end positions, labels, graphics parameters, and drawing options.

```APIDOC
## xscale

### Description
Defines x-scale visualization on tracks.

### Slots
- **from** (pos) - Start position.
- **to** (pos) - End position.
- **label** (character) - Scale label.
- **gp** (list) - Graphics parameters.
- **draw** (logical) - Whether to draw the scale.

### Methods
- `setTrackXscaleParam(track, param, value)` — Modify x-scale parameters.
```

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

### Creating a Position Object

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Shows how to construct a 'pos' object, which represents a point location with x, y coordinates and a specified unit system.

```r
pos(x=100, y=0.5, unit="native")
```

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

### Get Sequence Levels with seqlevels()

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/s4-methods-reference.md

Retrieve chromosome or sequence names from a track or trackList object. For trackList, it returns the seqlevels from the first track.

```r
chrs <- seqlevels(track)
# c("chr1", "chr2", "chr3", ...)

chrs_list <- seqlevels(trackList)
# Returns seqlevels from first track
```

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

### Create custom trackStyle

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Initializes a trackStyle object with specific visual parameters like track type, colors, and height. Requires the 'new' function.

```r
# Create custom style
style <- new("trackStyle",
             tracktype="histogram",
             color=c("red", "blue"),
             height=0.3,
             ylim=c(0, 100))
```

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

### Get Giemsa Stain Colors

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-utilities.md

Retrieves the standard Giemsa stain color scheme used for ideograms. This can be used to customize ideogram plotting.

```r
colors <- gieStain()
# Use in ideogramPlot
ideogramPlot(ideo, dataList, colorSheme=gieStain())
```

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

### Comprehensive trackViewer Usage Pattern

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Illustrates a complete workflow for using the trackViewer package, from importing data and customizing track styles to plotting tracks with viewer-specific styles.

```r
library(trackViewer)

# 1. Create tracks from data
track1 <- importScore("data1.bed", format="BED")
track2 <- importScore("data2.bw", format="BigWig")

# 2. Customize track styles
setTrackStyleParam(track1, "color", c("red", "darkred"))
setTrackStyleParam(track1, "tracktype", "histogram")
setTrackYaxisParam(track1, "label", TRUE)

# 3. Create track list with heights
tracks <- trackList(track1=track1, track2=track2, heightDist=c(2, 1))

# 4. Create viewer style
viewer_style <- trackViewerStyle(margin=c(.05, .1, .02, 0), xaxis=TRUE)

# 5. Plot tracks
gr <- GRanges("chr1", IRanges(1000000, 2000000))
viewTracks(tracks, gr=gr, viewerStyle=viewer_style, autoOptimizeStyle=TRUE)
```

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

### Add Gene Annotations to Tracks

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/README.md

Incorporate gene annotations into your tracks using a TxDb object. This example uses known human genes (hg19).

```r
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
olds <- c("3312", "390259")
tracks <- geneTrack(ids, TxDb.Hsapiens.UCSC.hg19.knownGene)
```

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

### Get Sequence Level Style with seqlevelsStyle()

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/s4-methods-reference.md

Determine the naming style of chromosome names (e.g., 'UCSC', 'Ensembl'). This is useful for understanding how sequence identifiers are formatted.

```r
style <- seqlevelsStyle(track)
# "UCSC"
```

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

### Create nested trackList

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Demonstrates creating a hierarchical trackList by nesting one trackList within another. This allows for grouping of tracks.

```r
# Nested structure
tl <- trackList(trackList(tr1, tr2), tr3)
```

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

### List Chromosomes and Navigate

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/common-patterns.md

Import a BigWig track, list all available chromosomes, and then plot data for the first few chromosomes. Use `Sys.sleep` to pause between plots.

```r
library(trackViewer)

# Import track
track <- importScore("data.bw", format="BigWig")

# Get all chromosomes
chroms <- listChromosomes(track)
print(chroms)  # c("chr1", "chr2", ..., "chrX", "chrY")

# Get location of specific position
# (useful for finding genes, peaks, etc.)
loc <- getLocation(track, pos=1000)

# Plot different regions
for(chrom in chroms[1:5]) {  # First 5 chromosomes
    gr <- GRanges(chrom, IRanges(1e6, 2e6))
    viewTracks(trackList(track), gr=gr)
    Sys.sleep(1)  # Pause between plots
}
```

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

### setTrackXscaleParam

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/s4-methods-reference.md

Modifies an x-scale attribute of a track. This function allows customization of the track's horizontal scale, including its start and end positions, label, and graphical parameters.

```APIDOC
## setTrackXscaleParam

### Description
Modifies an x-scale attribute of a track. This function allows customization of the track's horizontal scale, including its start and end positions, label, and graphical parameters.

### Signature
```r
setTrackXscaleParam(ts, attr, value)
```

### Parameters
#### Path Parameters
- **ts** (track) - Required - Track object to modify
- **attr** (character) - Required - Attribute name
- **value** (any) - Required - New value

### Available Attributes
- **from** (pos) - Starting position
- **to** (pos) - Ending position
- **label** (character) - Scale label text
- **gp** (list) - Graphics parameters
- **draw** (logical) - Whether to draw the scale
- **position** (list) - Special: list(x, y, label) for auto-positioning

### Position Attribute
When `attr="position"`, value must be a list:
```r
setTrackXscaleParam(track, "position", 
                   list(x=122929675, y=4, label=500))
```
This creates a scale bar at position x with the specified label.

### Returns
The modified track object (invisibly).

### Examples
```r
# Draw x-scale
setTrackXscaleParam(track, "draw", TRUE)

# Set scale label
setTrackXscaleParam(track, "label", "1 Mb")

# Set graphics parameters
setTrackXscaleParam(track, "gp", list(col="blue", lwd=2))

# Auto-position scale bar
setTrackXscaleParam(track, "position", 
                   list(x=1500000, y=0.5, label=500000))
```
```

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

### Track Configuration Methods

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/README.md

Methods for configuring track, x-scale, y-axis, and viewer styles.

```APIDOC
## Track Configuration Methods

- `setTrackStyleParam(track, attr, value)`: Modifies a style attribute of a `track` object.
- `setTrackXscaleParam(track, attr, value)`: Modifies an attribute of the x-scale for a `track` object.
- `setTrackYaxisParam(track, attr, value)`: Modifies an attribute of the y-axis for a `track` object.
- `setTrackViewerStyleParam(tvs, attr, value)`: Modifies an attribute of the `trackViewerStyle` object.
```

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

### Set Track Style Parameter

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/s4-methods-reference.md

Use to modify a specific style attribute of a track. Examples include changing the track type, setting colors, or adjusting y-axis limits.

```r
setTrackStyleParam(track, "tracktype", "histogram")
```

```r
setTrackStyleParam(track, "color", c("red", "blue"))
```

```r
setTrackStyleParam(track, "ylim", c(0, 100))
```

```r
setTrackStyleParam(track, "ylabpos", "right")
```

```r
setTrackStyleParam(track, "ylabgp", list(cex=0.8, col="blue"))
```

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

### Annotate 3D Chromatin Interactions with Lines

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-visualization.md

Adds annotations for 3D chromatin interactions or TADs to plots using lines. This example demonstrates reading interaction data and visualizing it with custom line styles.

```r
library(trackViewer)
library(InteractionSet)
gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds",
              package="trackViewer"))
tads <- GInteractions(
  GRanges("chr6", IRanges(c(51130001, 51130001, 51450001, 52210001), width=20000)),
  GRanges("chr6", IRanges(c(51530001, 52170001, 52210001, 53210001), width=20000)))
range <- GRanges("chr6", IRanges(51120000, 53200000))
tr <- gi2track(gi)
viewTracks(trackList(tr), gr=range, autoOptimizeStyle=TRUE)
addInteractionAnnotation(tads, "tr", grid.lines,
                         gp=gpar(col="#E69F00", lwd=3, lty=3))
```

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

### Import Paired WIG Files for Back-to-Back Visualization

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-core.md

Imports two WIG files for back-to-back visualization, populating both `dat` and `dat2` slots. A specific genomic range is also applied.

```r
wigfile1 <- system.file("extdata", "cpsf160.repA_+.wig", package="trackViewer", mustWork=TRUE)
wigfile2 <- system.file("extdata", "cpsf160.repA_-.wig", package="trackViewer", mustWork=TRUE)
dat <- importScore(wigfile1, wigfile2, format="WIG",
                   ranges=GRanges("chr11", IRanges(122817703, 122889073)))
```

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

### Display Track Object Summary

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/s4-methods-reference.md

The show method displays a summary of a track object, including its slots and their contents. This is helpful for inspecting the structure and data within a track.

```r
show(track)
# Output:
# This is an object of track
# slot name: Sample1
# slot type: data
# slot format: BED
# slot dat:
# GRanges object with N ranges and 1 metadata column
# ...
# slot dat2:
# GRanges object with 0 ranges and 0 metadata columns
# slot style: try object$style to see details.
```

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

### Access and modify track slots

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Demonstrates using the $ operator to access and modify slots within a track object, including GRanges data and track style. Also shows how to get and set sequence level information.

```r
# Extract slots using $ operator
track$dat        # Access GRanges data
track$style      # Access track style
track$type       # Access track type

# Set slots using $<- operator
track$dat <- GRanges(...)

# Get sequence information
seqlevels(track)      # Get chromosome names
seqlevelsStyle(track) # Get style of chromosome names

# Set sequence style
seqlevelsStyle(track) <- "UCSC"  # Set to UCSC format (chr1, chr2, ...)
```

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

### Use Auto-Optimization for Styles (R)

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/common-patterns.md

Enables automatic optimization of track styles for better visualization performance.

```r
# Let trackViewer optimize styles automatically
viewTracks(tracks, gr=gr, autoOptimizeStyle=TRUE)
```

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

### Interactive HTML Widget Visualization

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Demonstrates how to generate an interactive HTML widget for exploring genomic tracks using browseTracks. This allows for zooming, panning, and tooltips.

```R
library(trackViewer)

# Example: Create an interactive track viewer
track1 <- importScore("path/to/data1.bw")
track2 <- importScore("path/to/data2.bed")

browser <- browseTracks(trackList = list(track1, track2))

# To save the widget to an HTML file:
# htmlwidgets::saveWidget(browser, "interactive_tracks.html")
```

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

### Plot Genomic Tracks with viewTracks

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-visualization.md

Use this function to plot a collection of genomic tracks for a specified region. It requires a list of tracks and either a GRanges object or chromosome, start, and end coordinates. Strand information can be ignored or used for filtering.

```r
extdata <- system.file("extdata", package="trackViewer", mustWork=TRUE)
files <- dir(extdata, "-.wig")
tracks <- lapply(paste(extdata, files, sep="/"), 
                 importScore, format="WIG")
tracks <- lapply(tracks, function(.ele) {strand(.ele@dat) <- "-"; .ele})
fox2 <- importScore(paste(extdata, "fox2.bed", sep="/"), format="BED")
dat <- coverageGR(fox2@dat)
fox2@dat <- dat[strand(dat)=="+"]
fox2@dat2 <- dat[strand(dat)=="-"]
gr <- GRanges("chr11", IRanges(122929275, 122930122), strand="-")
viewTracks(trackList(track=tracks, fox2=fox2), gr=gr, autoOptimizeStyle=TRUE)
```

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

### Plotting Genomic Data on Ideograms

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-visualization.md

This example demonstrates how to plot genomic data on chromosome ideograms using the ideogramPlot function. It requires loading ideogram coordinates and preparing data as a GRangesList. Custom layouts and plotting parameters like heatmap type and color key title can be specified.

```r
ideo <- loadIdeogram("hg38")
library(rtracklayer)
library(grid)
dataList <- ideo
dataList$score <- as.numeric(dataList$gieStain)
dataList <- dataList[dataList$gieStain!="gneg"]
dataList <- GRangesList(dataList)
grid.newpage()
ideogramPlot(ideo, dataList, 
             layout=list("chr1", "chr2", c("chr3", "chr22"), 
                         c("chr4", "chr21"), c("chr5", "chr20"), 
                         c("chr6", "chr19"), c("chr7", "chr18"),
                         c("chr8", "chr17"), c("chr9", "chr16"),
                         c("chr10", "chr15"), c("chr11", "chr14"),
                         c("chr12", "chr13"), c("chrX", "chrY")),
             parameterList = list(types="heatmap", colorKeyTitle="sample1"))
```

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

### Import WIG File

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-core.md

Imports data from a WIG file. The format parameter is explicitly set to 'WIG'.

```r
wigfile <- system.file("tests", "step.wig", package="rtracklayer", mustWork=TRUE)
dat <- importScore(file=wigfile, format="WIG")
```

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

### Precompute Styles for Reuse (R)

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/common-patterns.md

Defines custom track styles once and applies them to multiple tracks for consistent visualization.

```r
# Define styles once, reuse for multiple plots
style <- new("trackStyle",
            tracktype="histogram",
            color=c("blue", "blue"),
            ylim=c(0, 100))

track$style <- style
```

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

### Initialize and Modify Track Viewer Style

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/s4-methods-reference.md

Initializes a track viewer style object and demonstrates setting various style parameters like margins, x-axis visibility, font, flipping, and label direction.

```r
tvs <- trackViewerStyle()

# Set margins
setTrackViewerStyleParam(tvs, "margin", c(.05, .1, .02, 0))

# Enable x-axis
setTrackViewerStyleParam(tvs, "xaxis", TRUE)

# Set x-axis font
setTrackViewerStyleParam(tvs, "xgp", list(cex=0.7))

# Flip x-axis
setTrackViewerStyleParam(tvs, "flip", TRUE)

# Set label direction
setTrackViewerStyleParam(tvs, "xlas", 2)
```

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

### Access trackViewer Vignettes

Source: https://github.com/jianhong/trackviewer/blob/devel/README.md

Open the package documentation vignettes in a web browser.

```r
browseVignettes("trackViewer")
```

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

### Create trackList with equal heights

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Constructs a trackList with multiple tracks, assigning equal heights by default. Requires pre-defined track objects (e.g., tr1, tr2, tr3).

```r
# Create a track list with equal heights
tl <- trackList(track1=tr1, track2=tr2, track3=tr3)
```

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

### Create trackList with custom height distribution

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Constructs a trackList with specified relative heights for each track. The heightDist parameter normalizes the provided ratios to sum to 1.

```r
# Create with custom height distribution (3:1:2 ratio)
tl <- trackList(track1=tr1, track2=tr2, track3=tr3, heightDist=c(3, 1, 2))
```

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

### List Normalization Methods in Hi-C File

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-utilities.md

Lists available normalization methods for a given Hi-C file. Requires the path to the HDF5 formatted file.

```r
listNormalizations(file)
```

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

### Initialize Track Viewer Style

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

Constructs a new trackViewerStyle object with default or specified parameters for margins, axis labels, and graphics.

```r
trackViewerStyle(margin=c(.01, .05, 0, 0),
                 xlas=0,
                 xgp=list(),
                 xaxis=FALSE,
                 xat=numeric(0),
                 xlabel=character(0),
                 autolas=FALSE,
                 flip=FALSE)
```

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

### show

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/s4-methods-reference.md

Displays a summary of a track object, including its slots and their contents.

```APIDOC
## show

### Description
Displays a summary of a track object, including its slots and their contents.

### Signature
```r
show(object)
```

### Examples
```r
show(track)
# Output:
# This is an object of track
# slot name: Sample1
# slot type: data
# slot format: BED
# slot dat:
# GRanges object with N ranges and 1 metadata column
# ...
# slot dat2:
# GRanges object with 0 ranges and 0 metadata columns
# slot style: try object$style to see details.
```
```

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

### Visualize Strand-Specific Data

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/README.md

Import forward and reverse strand WIG data, create a back-to-back track, set colors, and visualize using viewTracks.

```r
# Import forward and reverse strand data
forward <- importScore("forward.wig", format="WIG")
reverse <- importScore("reverse.wig", format="WIG")

# Create back-to-back track
track <- new("track", 
             dat=forward@dat,
             dat2=reverse@dat,
             type="data",
             format="WIG")
setTrackStyleParam(track, "color", c("green", "red"))
setTrackStyleParam(track, "tracktype", "histogram")

viewTracks(trackList(track), gr=region)
```

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

### Create and Modify trackViewerStyle

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Demonstrates how to create a trackViewerStyle object with custom margins and axis settings, and how to modify its parameters after creation using setTrackViewerStyleParam.

```r
trackViewerStyle()
trackViewerStyle(margin=c(.02, .05, 0, 0), xaxis=TRUE)
```

```r
# Create with custom margins
tvs <- trackViewerStyle(margin=c(.05, .1, 0.01, 0), xaxis=TRUE)

# Modify after creation
setTrackViewerStyleParam(tvs, "xaxis", TRUE)
setTrackViewerStyleParam(tvs, "margin", c(.05, .1, .02, 0))
```

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

### Class Constructors

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/README.md

Constructors for creating core TrackViewer objects.

```APIDOC
## Class Constructors

- `trackList()`: Creates an empty track list.
- `trackViewerStyle()`: Creates a track viewer style object.
```

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

### importScore Parameters

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

Parameters for importing score files like BED, bedGraph, WIG, or BigWig.

```APIDOC
## importScore Parameters

### Description
Imports score data from a specified file.

### Parameters
#### Path Parameters
- **file** (character) - Required - File path to import
- **file2** (character) - Optional - Second file for paired data

#### Query Parameters
- **format** (character) - Optional - File format (default: "BED", accepted: "BED", "bedGraph", "WIG", "BigWig")
- **ranges** (GRanges) - Optional - Genomic region(s) to import (default: empty GRanges)
- **ignore.strand** (logical) - Optional - Ignore strand when filtering (default: TRUE)
```

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

### trackStyle Constructor

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

Initializes a new trackStyle object with default or specified parameters. This object defines the visual appearance of a track.

```APIDOC
## trackStyle Constructor

### Description
Initializes a new trackStyle object with default or specified parameters. This object defines the visual appearance of a track.

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Constructor Signature
```r
new("trackStyle",
    tracktype="peak",
    color=c("black", "black"),
    NAcolor="white",
    breaks=0,
    height=NA,
    marginTop=0,
    marginBottom=0.05,
    xscale=new("xscale"),
    yaxis=new("yaxisStyle"),
    ylim=NA,
    ylabpos="left",
    ylablas=0,
    ylabgp=list(),
    ysplit=0.5)
```

### Parameter Details
- **tracktype** (character) - Required/Optional - Track visualization type. Default: "peak"
- **color** (character) - Required/Optional - Color(s) for track; 2 for paired. Default: c("black", "black")
- **NAcolor** (character) - Required/Optional - Color for NA values in heatmap. Default: "white"
- **breaks** (numeric) - Required/Optional - Heatmap color scale breaks. Default: 0
- **height** (numeric) - Required/Optional - Height as fraction [0,1]. Default: NA
- **marginTop** (numeric) - Required/Optional - Top margin. Default: 0
- **marginBottom** (numeric) - Required/Optional - Bottom margin. Default: 0.05
- **xscale** (xscale) - Required/Optional - X-scale configuration. Default: new("xscale")
- **yaxis** (yaxisStyle) - Required/Optional - Y-axis configuration. Default: new("yaxisStyle")
- **ylim** (numeric) - Required/Optional - Y-axis limits. Default: NA
- **ylabpos** (character) - Required/Optional - Y-label position. Default: "left"
- **ylablas** (numeric) - Required/Optional - Y-label orientation (0-3). Default: 0
- **ylabgp** (list) - Required/Optional - Y-label graphics parameters. Default: list()
- **ysplit** (numeric) - Required/Optional - Y-split ratio for interactions. Default: 0.5
```

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

### importGInteractions Parameters

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

Parameters for importing interaction files, with options for normalization and resolution.

```APIDOC
## importGInteractions Parameters

### Description
Imports interaction data from a file.

### Parameters
#### Path Parameters
- **file** (character) - Required - Interaction file path

#### Query Parameters
- **ranges** (GRanges) - Optional - Genomic region(s) to import (default: empty GRanges)
- **format** (character) - Optional - File format (default: NA)
- **norm** (character) - Optional - Normalization method (Hi-C files) (default: NA)
- **resolution** (numeric) - Optional - Resolution/bin size (Hi-C files) (default: NA)
```

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

### Render BrowseTracks Widget

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-visualization.md

Renders an existing browseTracks htmlwidget. Requires the widget object and a target HTML div ID.

```r
renderbrowseTracks(x, div_id, ...)
```

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

### importBam Parameters

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

Parameters for importing BAM files, including options for paired-end reads.

```APIDOC
## importBam Parameters

### Description
Imports data from BAM files.

### Parameters
#### Path Parameters
- **file** (character) - Required - BAM file path
- **file2** (character) - Optional - Second BAM file for paired data

#### Query Parameters
- **ranges** (GRanges) - Optional - Genomic region(s) to import (default: empty GRanges)
- **pairs** (logical) - Optional - Whether reads are paired-end (default: FALSE)
```

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

### Smoothed Signal Visualization

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Demonstrates how to visualize smoothed signal data. Smoothing can help in reducing noise and highlighting trends in genomic signal tracks.

```R
library(trackViewer)

# Example: Visualize a smoothed signal track
signal_track <- importScore("path/to/noisy_signal.bw")

# Smoothing might be applied during import or as a separate step
# For example, using a rolling mean if the data allows
# smoothed_signal <- ... # calculation of smoothed signal

# Assuming smoothed_signal is a track object
viewTracks(trackList = list(smoothed_signal))
```

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

### Visualize ChIP-seq Peaks and Coverage

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/README.md

Import BED peaks and WIG background coverage, set track styles, add gene annotations, and plot them together using TxDb and geneModelFromTxdb.

```r
# Import peaks and compute coverage
peaks <- importScore("peaks.bed", format="BED")
setTrackStyleParam(peaks, "tracktype", "peak")
setTrackStyleParam(peaks, "color", c("darkblue", "darkblue"))

# Import background coverage
bkgd <- importScore("background.wig", format="WIG")
setTrackStyleParam(bkgd, "tracktype", "histogram")
setTrackStyleParam(bkgd, "color", c("gray", "gray"))

# Add gene annotation
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
genes <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene, 
                           org.Hs.eg.db, gr=region)

# Plot together
tracks <- trackList(peaks=peaks, coverage=bkgd, genes=genes)
viewTracks(tracks, gr=region, autoOptimizeStyle=TRUE)
```

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

### Import BED, bedGraph, WIG, BigWig Files

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Use importScore to import genomic data files. Ensure files are in BED, bedGraph, WIG, or BigWig format.

```R
importScore(file = "path/to/your/file.bed")
```

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

### Basic Track Visualization

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/common-patterns.md

Use this pattern to visualize a single genomic track from a BED file within a specified region. Ensure the trackViewer library is loaded.

```r
library(trackViewer)

# Import data
track <- importScore("data.bed", format="BED")

# Specify region to display
gr <- GRanges("chr1", IRanges(1000000, 2000000))

# Plot
viewTracks(trackList(track), gr=gr)
```

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

### Import BAM Files with Coverage

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Use importBam to import BAM files and generate coverage tracks. This function is useful for visualizing alignment data.

```R
importBam(file = "path/to/your/file.bam")
```

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

### Hi-C Utilities

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Use listResolutions and listNormalizations for Hi-C data utilities. These functions help in exploring Hi-C experiment parameters.

```R
listResolutions(genome = "hg19")
```

```R
listNormalizations(genome = "hg19")
```

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

### Compute Ratios of BigWig Tracks

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/common-patterns.md

Use the 'operator' argument in viewTracks to compute ratios between imported BigWig samples. Ensure samples are imported using importScore.

```r
library(trackViewer)

# Import two samples
sample1 <- importScore("sample1.bw", format="BigWig")
sample2 <- importScore("sample2.bw", format="BigWig")

# Plot with operator to show ratio
gr <- GRanges("chr1", IRanges(1e6, 2e6))

# Divide scores: sample1 / sample2
viewTracks(trackList(sample1, sample2), 
          gr=gr,
          operator=c("/", "/"))  # Apply division operator
```

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

### Custom Style Optimization

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Demonstrates the use of optimizeStyle to automatically adjust track styles for better visual presentation. This function can help in managing complex track layouts.

```R
library(trackViewer)

# Example: Optimize styles for a list of tracks
track1 <- importScore("path/to/track1.bw")
track2 <- importScore("path/to/track2.bed")

trackList <- list(track1, track2)

optimized_tracks <- optimizeStyle(trackList = trackList)
viewTracks(trackList = optimized_tracks)
```

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

### List Resolutions in Hi-C File

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-utilities.md

Lists available resolutions (bin sizes) for a given Hi-C file. Requires the path to the HDF5 formatted file.

```r
listResolutions(file)
```

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

### Configure Strand-Specific Track

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

Sets up a track for strand-specific data, importing two WIG files for forward and reverse strands. Configures the track type and colors for each strand.

```R
track <- importScore("forward.wig", "reverse.wig", format="WIG")
setTrackStyleParam(track, "color", c("darkgreen", "darkred"))
setTrackStyleParam(track, "tracktype", "histogram")
```

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

### browseTracks

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-visualization.md

Creates an interactive HTML widget for browsing genomic tracks. It returns an htmlwidget object that displays tracks interactively.

```APIDOC
## browseTracks

### Description
Creates an interactive HTML widget for browsing genomic tracks.

### Signature
```r
browseTracks(trackList, 
             gr=GRanges(),
             ignore.strand=TRUE,
             width=NULL, height=NULL, 
             ...)
```

### Parameters
#### Arguments
- **trackList** (trackList or list) - Required - Collection of track objects to display.
- **gr** (GRanges) - Required - Region to display.
- **ignore.strand** (logical) - TRUE - Ignore strand when filtering tracks.
- **width** (integer) - NULL - Width of the HTML widget in pixels.
- **height** (integer) - NULL - Height of the HTML widget in pixels.
- **...** (any) - Unused - Additional parameters.

### Returns
An htmlwidget object that displays tracks interactively in a web browser or R Markdown document.

### Throws
- Error if gr is not a GRanges object
- Error if gr length is not 1
- Error if trackList is missing in non-interactive sessions

### Examples
```r
extdata <- system.file("extdata", package="trackViewer", mustWork=TRUE)
files <- dir(extdata, "-.wig")
tracks <- lapply(paste(extdata, files, sep="/"), 
                 importScore, format="WIG")
tracks <- lapply(tracks, function(.ele) {strand(.ele@dat) <- "-"; .ele})
names(tracks) <- c("trackA", "trackB")
fox2 <- importScore(paste(extdata, "fox2.bed", sep="/"), format="BED")
dat <- coverageGR(fox2@dat)
fox2@dat <- dat[strand(dat)=="+"]
fox2@dat2 <- dat[strand(dat)=="-"]
gr <- GRanges("chr11", IRanges(122929275, 122930122))
browseTracks(trackList(tracks, fox2), gr=gr)
```
```

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

### Import BAM Files

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

Use importBam to load data from BAM files. Provide the BAM file path, and optionally a second file for paired-end data, genomic ranges, and a flag indicating if the reads are paired.

```r
importBam(file, file2, 
          ranges=GRanges(), 
          pairs=FALSE)
```

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

### Configure Margin for Track Viewer Style

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/configuration.md

Sets the margin parameters (bottom, left, top, right) for the track viewer style.

```r
setTrackViewerStyleParam(tvs, "margin", c(.05, .1, .02, 0))
```

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

### Create a track object

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Constructs a new 'track' object using the 'new' function. Requires GRanges data, track type, and input format.

```r
track <- new("track", 
             dat=GRanges(...), 
             type="data", 
             format="BED")
```

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

### listResolutions(file)

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-utilities.md

Lists available resolutions in a Hi-C file. This function is useful for understanding the different granularities at which Hi-C data is stored.

```APIDOC
## listResolutions(file)

### Description
Lists available resolutions in a Hi-C file.

### Parameters
#### Path Parameters
- **file** (character) - Required - Path to Hi-C file (HDF5 format)

### Returns
A numeric vector of available resolutions (bin sizes).
```

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

### Sequence Level Methods

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Reference for seqlevels() and seqlevelsStyle() methods for managing chromosome naming and styles. seqlevelsStyle()<- allows setting the style.

```R
seqlevels(myGRangesObject)
```

```R
seqlevelsStyle(myGRangesObject)
```

```R
seqlevelsStyle(myGRangesObject) <- "UCSC"
```

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

### Access tracks in trackList

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-classes.md

Shows how to access individual tracks within a trackList by their index or name. Assumes a trackList object 'tl' has been created.

```r
# Access tracks
first_track <- tl[[1]]
track_by_name <- tl(("track1"))
```

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

### Annotations (Guidelines, Arrows)

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Covers adding various types of annotations to track visualizations, including vertical guidelines and arrows. These annotations help in highlighting specific features or regions of interest.

```R
library(trackViewer)

# Example: Add a guideline and an arrow
track_data <- importScore("path/to/data.bw")

# Add a vertical guideline at position 1,000,000
plot_with_guideline <- addGuideLine(position = 1000000)

# Add an arrow annotation
plot_with_arrow <- addArrowMark(start = 500000, end = 700000, direction = "reverse")

# Combine annotations (conceptual - actual implementation depends on viewTracks usage)
viewTracks(trackList = list(track_data), annotations = list(plot_with_guideline, plot_with_arrow))
```

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

### listNormalizations(file)

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-utilities.md

Lists available normalization methods in a Hi-C file. This function helps identify compatible normalization strategies for Hi-C data analysis.

```APIDOC
## listNormalizations(file)

### Description
Lists available normalization methods in a Hi-C file.

### Parameters
#### Path Parameters
- **file** (character) - Required - Path to Hi-C file (HDF5 format)

### Returns
A character vector of available normalization methods.
```

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

### Class Definitions

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Reference for the core classes used in TrackViewer, including their slots and methods.

```APIDOC
## track class

### Description
Represents a single genomic track, including its data, styling, and display properties.

### Slots
- **data** (object) - The genomic data for the track.
- **style** (trackStyle object) - Styling options for the track.
- **...** - Other slots defining track properties.

### Constructor
Provides constructor signatures and examples for creating track objects.

### Accessor Methods
Defines accessor methods for retrieving slot values.

## trackList class

### Description
Manages a collection of track objects, supporting nesting and ordering.

### Slots
- **tracks** (list) - A list of track objects.
- **...** - Other slots for list management.

### Constructor
Provides constructor signatures and examples for creating trackList objects.

### Accessor Methods
Defines accessor methods for retrieving trackList properties.

## trackStyle class

### Description
Defines styling options for a genomic track.

### Slots
- **color** (string) - Track color.
- **height** (numeric) - Track height.
- **...** - All available styling parameters.

### Constructor
Provides constructor signatures and examples for creating trackStyle objects.

### Accessor Methods
Defines accessor methods for styling attributes.

## trackViewerStyle class

### Description
Configuration for the overall track viewer appearance and behavior.

### Slots
- **width** (numeric) - Viewer width.
- **height** (numeric) - Viewer height.
- **...** - Viewer configuration options.

### Constructor
Provides constructor signatures and examples for trackViewerStyle objects.

### Accessor Methods
Defines accessor methods for viewer style attributes.

## xscale, yaxisStyle, pos helper classes

### Description
Helper classes for defining x-axis scaling, y-axis styling, and positional information.

### Constructor
Provides constructor signatures and examples for these helper classes.

### Accessor Methods
Defines accessor methods for their respective properties.
```

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

### importScore

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/api-reference-core.md

Reads a track object from BED, bedGraph, WIG, or BigWig files. It supports importing single or paired files for back-to-back visualization.

```APIDOC
## importScore

### Description
Reads a track object from a BED, bedGraph, WIG, or BigWig file. Supports importing single or paired files for back-to-back visualization.

### Signature
importScore(file, file2 = NULL, format = c("BED", "bedGraph", "WIG", "BigWig"), ranges = GRanges(), ignore.strand = TRUE)

### Parameters
#### Path Parameters
- **file** (character) - Required - Path to the file to read.
- **file2** (character) - Optional - Path to the second file to read (for paired tracks).

#### Query Parameters
- **format** (character) - Optional - File format: "BED", "bedGraph", "WIG", or "BigWig". Defaults to "BED".
- **ranges** (GRanges) - Optional - Genomic range to limit import scope. Defaults to an empty GRanges object.
- **ignore.strand** (logical) - Optional - Whether to ignore strand information when filtering. Defaults to TRUE.

### Returns
An object of class `track` with data read from the specified file(s). If `file2` is provided, returns a track with both `dat` and `dat2` slots populated for back-to-back visualization.

### Throws
- Error if `ranges` is not a GRanges object.
- Error if `format` is not one of the supported formats.
- Error if file format does not match the specified format parameter.

### Request Example
```r
# Import a BED file
bedfile <- system.file("tests", "test.bed", package="rtracklayer", mustWork=TRUE)
dat <- importScore(file=bedfile, format="BED",
                   ranges=GRanges("chr7", IRanges(127471197, 127474697)))

# Import a WIG file
wigfile <- system.file("tests", "step.wig", package="rtracklayer", mustWork=TRUE)
dat <- importScore(file=wigfile, format="WIG")

# Import two paired files for back-to-back visualization
wigfile1 <- system.file("extdata", "cpsf160.repA_+.wig", package="trackViewer", mustWork=TRUE)
wigfile2 <- system.file("extdata", "cpsf160.repA_-.wig", package="trackViewer", mustWork=TRUE)
dat <- importScore(wigfile1, wigfile2, format="WIG",
                   ranges=GRanges("chr11", IRanges(122817703, 122889073)))
```
```

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

### Back-to-Back (Strand-Specific) Visualization

Source: https://github.com/jianhong/trackviewer/blob/devel/_autodocs/COMPLETION_SUMMARY.txt

Demonstrates how to create back-to-back plots, which are useful for visualizing strand-specific data, such as gene expression or methylation levels on forward and reverse strands.

```R
library(trackViewer)

# Example: Visualize strand-specific data
strand_data <- importScore("path/to/strand_data.wig")

# Assuming strand_data has strand information
viewTracks(trackList = list(strand_data), type = "backtoback")
```