### Example: Reshowing Page Guides - plotgardener

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/pageGuideShow.html

This example demonstrates the typical workflow of creating a page, adding guides, plotting data, hiding guides, and then reshowing them. Ensure the plotgardenerData package is loaded and data is available.

```r
library(plotgardenerData)
data("IMR90_HiC_10kb")

pageCreate(width = 3, height = 3, default.units = "inches")

pageGuideHorizontal(y = 0.5, default.units = "inches")

hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb,
    resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    x = 0.5, y = 0.5, width = 2, height = 2,
    just = c("left", "top"),
    default.units = "inches"
)

pageGuideHide()

pageGuideShow()

annoGenomeLabel(
    plot = hicPlot, scale = "Mb", axis = "x",
    x = 0.5, y = 2.53, just = c("left", "top")
)
```

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

### Load Example Data for Multi-omic Plotting

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotting_multiomic_data.html

Loads necessary datasets for plotting multi-omic data. Ensure plotgardenerData is installed.

```R
library(plotgardenerData)
data("IMR90_HiC_10kb")
data("IMR90_DNAloops_pairs")
data("IMR90_ChIP_H3K27ac_signal")
data("hg19_insulin_GWAS")
```

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

### Place a Hi-C Plot on a Page

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/pagePlotPlace.html

This example demonstrates how to create a Hi-C plot object without drawing it, then place it onto a plotgardener page with specified dimensions and justification. It also shows how to add a heatmap legend and hide page guides.

```R
library(plotgardenerData)
data("IMR90_HiC_10kb")

hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    draw = FALSE
)

pageCreate(width = 3.75, height = 3.5, default.units = "inches")

pagePlotPlace(
    plot = hicPlot,
    x = 0.25, y = 0.25, width = 3, height = 3,
    just = c("left", "top"),
    default.units = "inches", draw = TRUE
)

annoHeatmapLegend(
    plot = hicPlot,
    x = 3.4, y = 0.25, width = 0.12, height = 1.2,
    just = c("left", "top"), default.units = "inches"
)

pageGuideHide()
```

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

### Install plotgardener and plotgardenerData

Source: https://github.com/phanstiellab/plotgardener/blob/devel/README.md

Installs the plotgardener package and its associated data package from Bioconductor. Ensure BiocManager is installed first.

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(version = "3.19")

BiocManager::install("plotgardener")

```

```r
BiocManager::install("plotgardenerData")

```

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

### Load Example Data

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotting_multiomic_data.html

Loads necessary datasets for multi-omic plotting. Ensure these datasets are available in your R environment.

```R
data("IMR90_HiC_10kb")
data("IMR90_DNAloops_pairs")
data("IMR90_ChIP_H3K27ac_signal")
data("hg19_insulin_GWAS")
```

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

### Show Page Guides - plotgardener

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/pageGuideShow.html

Use this function to reshow page guides that have been hidden. It does not require any arguments.

```r
pageGuideShow()
```

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

### Reshow Page Guides

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/pageGuideShow.html

This snippet demonstrates how to use the pageGuideShow() function to make previously hidden page guides visible again. It's typically called after pageGuideHide().

```APIDOC
## pageGuideShow()

### Description
Reshow guides drawn with `pageCreate`, `pageGuideHorizontal`, and `pageGuideVertical`.

### Method
`pageGuideShow()`

### Parameters
None

### Value
None.

### See also
[pageCreate](pageCreate.html), [pageGuideHorizontal](pageGuideHorizontal.html), [pageGuideVertical](pageGuideVertical.html)

### Examples

```R
## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create a page
pageCreate(width = 3, height = 3, default.units = "inches")

## Add a page guide
pageGuideHorizontal(y = 0.5, default.units = "inches")

## Plot and place Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb,
    resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000,
    chromend = 30300000,
    x = 0.5,
    y = 0.5,
    width = 2,
    height = 2,
    just = c("left", "top"),
    default.units = "inches"
)

## Hide page guides
pageGuideHide()


## Re-show page guides
pageGuideShow()

## Annotate genome label
annoGenomeLabel(
    plot = hicPlot,
    scale = "Mb",
    axis = "x",
    x = 0.5,
    y = 2.53,
    just = c("left", "top")
)
```
```

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

### Example: Plot Hi-C Data with Heatmap Legend

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/annoHeatmapLegend.html

Demonstrates plotting Hi-C data and adding a heatmap legend. Requires loading plotgardenerData and creating a plot page.

```R
## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create page
pageCreate(width = 4, height = 3.5, default.units = "inches")

## Plot and place a square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb,
    resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",

```

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

### Download and Read .cool file

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/readCool.html

Demonstrates how to download an example .cool file and read a specific region with a given resolution. Ensure the file path and region parameters are correctly set for your data.

```R
coolFile <- file.path(tempdir(), "Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool")
download.file(url = "https://usgs2.osn.mghpcc.org/cooler01/examples/hg19/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool",
    destfile = coolFile, mode = "wb")

## Read in region `chr2:10000000-22000000` at 1000Kb cool file resolution
coolData <- readCool(file = coolFile, chrom = "chr2", chromstart = 10000000,
                     chromend = 22000000,
                     resolution = 1000000)
#> Read in .cool file with NONE normalization at 1e+06 BP resolution.
```

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

### Load and Inspect Sample Data

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotgardener_meta_functions.html

Loads the IMR90_ChIP_CTCF_reads dataset and displays the first few rows to show its structure, including columns like 'chrom', 'start', 'end', and 'strand'.

```r
data("IMR90_ChIP_CTCF_reads")
head(IMR90_ChIP_CTCF_reads)

```

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

### Load data and create plotgardener page

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotting_multiomic_data.html

Loads example multi-omic datasets and initializes a plotgardener page with specified dimensions and grid settings. Ensure necessary libraries are loaded before execution.

```R
## Load example data
data("IMR90_HiC_10kb")
data("IMR90_DNAloops_pairs")
data("IMR90_ChIP_H3K27ac_signal")
data("hg19_insulin_GWAS")

## Create a plotgardener page
pageCreate(
    width = 3, height = 5, default.units = "inches",
    showGuides = FALSE, xgrid = 0, ygrid = 0
)
```

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

### Get Default Packages for a Genome

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotgardener_meta_functions.html

Retrieves the default annotation packages (TxDb, OrgDb, etc.) associated with a specified genome build.

```r
defaultPackages("hg19")

```

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

### Create and Annotate Hi-C Plot

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/annoPixels.html

This example demonstrates loading Hi-C and loop data, creating a page, plotting a square Hi-C plot, and then annotating loops on both sides of the plot with squares.

```r
library(plotgardenerData)
data("IMR90_HiC_10kb")
data("IMR90_DNAloops_pairs")

## Create page
pageCreate(width = 4.5, height = 4, default.units = "inches")

## Plot and place a square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 0.5, width = 3, height = 3,
    just = c("left", "top"),
    default.units = "inches"
)
#> Read in dataframe.  Assuming 'chrom' in column1 and 'altchrom' in column2. 10000 BP resolution detected.
#> hicSquare[hicSquare1]

## Annotate loops of both sides of Hi-C plot with squares
pixels <- annoPixels(
    plot = hicPlot, data = IMR90_DNAloops_pairs, type = "box",
    half = "both"
)

#> pixel[pixel1]
```

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

### Plot rectangles with varied properties

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/plotRect.html

Shows how to plot rectangles with differing widths, heights, positions, and colors. This example also demonstrates setting `linecolor = NA` to remove borders and using `alpha` for transparency.

```R
plotRect(
    x = 3.75, y = c(4, 5.25), width = c(6.5, 4.5),
    height = c(1, 0.25),
    just = "top", default.units = "inches",
    fill = c("#7ecdbb", "#37a7db"), linecolor = NA, alpha = 0.4
)

#>
#> rect[rect2]
#
```

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

### Get Default Bioconductor Packages for an Assembly

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/bioconductor_integration.html

Retrieve the default TxDb, OrgDb, and BSgenome packages for a specified genomic assembly. Useful for setting up standard genomic annotations.

```R
defaultPackages("hg38")
#> 'data.frame':    1 obs. of  6 variables:
#>  $ Genome        : chr "hg38"
#>  $ TxDb          : chr "TxDb.Hsapiens.UCSC.hg38.knownGene"
#>  $ OrgDb         : chr "org.Hs.eg.db"
#>  $ gene.id.column: chr "ENTREZID"
#>  $ display.column: chr "SYMBOL"
#>  $ BSgenome      : chr "BSgenome.Hsapiens.UCSC.hg38"
```

```R
defaultPackages("hg19")
#> 'data.frame':    1 obs. of  6 variables:
#>  $ Genome        : chr "hg19"
#>  $ TxDb          : chr "TxDb.Hsapiens.UCSC.hg19.knownGene"
#>  $ OrgDb         : chr "org.Hs.eg.db"
#>  $ gene.id.column: chr "ENTREZID"
#>  $ display.column: chr "SYMBOL"
#>  $ BSgenome      : chr "BSgenome.Hsapiens.UCSC.hg19"
```

```R
defaultPackages("mm10")
#> 'data.frame':    1 obs. of  6 variables:
#>  $ Genome        : chr "mm10"
#>  $ TxDb          : chr "TxDb.Mmusculus.UCSC.mm10.knownGene"
#>  $ OrgDb         : chr "org.Mm.eg.db"
#>  $ gene.id.column: chr "ENTREZID"
#>  $ display.column: chr "SYMBOL"
#>  $ BSgenome      : chr "BSgenome.Mmusculus.UCSC.mm10"
```

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

### Download and Read .mcool file at 100Kb resolution

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/readCool.html

Shows how to download an example .mcool file and read a specific region at 100Kb resolution. This is useful for analyzing Hi-C data at finer scales. Note the chromosome is specified as '2' instead of 'chr2'.

```R
mcoolFile <- file.path(tempdir(), "LEUK_HEK_PJA27_inter_30.mcool")
download.file(url = "https://zenodo.org/records/10906240/files/LEUK_HEK_PJA27_inter_30.mcool?download=1",
    destfile = mcoolFile, mode = "wb")

## Read in region `chr2:1000000-5000000` at 100Kb resolution
mcoolData_100Kb <- readCool(file = mcoolFile, chrom = "2",
                            chromstart = 1000000, chromend = 5000000,
                            resolution = 100000)
#> Read in .mcool file with NONE normalization at 1e+05 BP resolution.
```

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

### Plotting Flipped Ideogram

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/plotIdeogram.html

This example demonstrates how to plot a chromosome ideogram with reversed start and end positions by setting 'flip' to TRUE. This effectively reverses the direction of the ideogram.

```R
library(plotgardener)

pag <- pageCreate()

# Plot flipped ideogram for chr1
plotIdeogram(chrom = "chr1", flip = TRUE)

pageDraw(pag)
```

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

### Create a Page and Add Vertical Guideline

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/pageGuideVertical.html

Demonstrates how to initialize a plotgardener page and then add a blue vertical guideline at a specific x-coordinate.

```R
pageCreate(width = 6, height = 5, default.units = "inches")
```

```R
pageGuideVertical(x = 1.7, linecolor = "blue")
```

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

### Plotting Ideogram with Custom Cytoband Data

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/plotIdeogram.html

This example shows how to plot a chromosome ideogram using custom cytoband data provided as a data frame. The data frame must include columns: 'seqnames', 'start', 'end', 'width', 'strand', 'name', 'gieStain'.

```R
library(plotgardener)

pag <- pageCreate()

# Define custom cytoband data (example for a small region)
custom_cytobands <- data.frame(
  seqnames = rep("chr1", 3),
  start = c(1000000, 5000000, 10000000),
  end = c(4000000, 9000000, 15000000),
  width = c(3000000, 4000000, 5000000),
  strand = rep(".", 3),
  name = paste0("band", 1:3),
  gieStain = c("gneg", "gpos50", "gpos25")
)

# Plot ideogram with custom data
plotIdeogram(chrom = "chr1", data = custom_cytobands)

pageDraw(pag)
```

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

### Hide Page Guides

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/pageGuideHide.html

This snippet demonstrates how to hide the guides on a plotgardener page after it has been created.

```APIDOC
## pageGuideHide()

### Description
Remove guides from a plotgardener page.

### Method
pageGuideHide()

### Parameters
None

### Response
None.

### Note
Due to the implementation of `grid` removal functions, using `pageGuideHide` within a `pdf` call will result in the rendering of a separate, new page with the plot guides removed. To avoid this artifact, hide guides in the `pageCreate` function call with `showGuides = FALSE`.

### Example
```R
## Make a page
pageCreate(width = 7, height = 4, default.units = "inches")

## Hide page guides
pageGuideHide()
```
```

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

### Create a Custom Sized Page with Custom Gridlines

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotgardener_page.html

Demonstrates creating a page with specified dimensions, units, and custom grid spacing using `pageCreate`.

```r
pageCreate(width = 8, height = 8, xgrid = 1, ygrid = 1, default.units = "cm")
```

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

### Hide Page Guides

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/annoHighlight.html

Hides the page guides, which are visual aids for plot layout.

```APIDOC
## pageGuideHide

### Description
Hides the page guides.

### Method
`pageGuideHide()`

### Parameters
None

### Returns
None
```

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

### Create a Page and Add Horizontal Guideline

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/pageGuideHorizontal.html

Demonstrates how to initialize a plotgardener page and add a horizontal guideline at a specific y-coordinate with a custom color.

```r
pageCreate(width = 6, height = 5, default.units = "inches")

## Add red horizontal guideline at y = 2.5 inches
pageGuideHorizontal(y = 2.5, linecolor = "red")
```

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

### Create and Plot Raster Images

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/ideograms_and_shapes.html

Demonstrates creating a page and plotting two raster images (pg_type and gene_gnome) at specified coordinates and dimensions. Ensure the 'plotgardener' package is loaded.

```R
library(plotgardener)

pageCreate(
    width = 5, height = 6, default.units = "inches",
    showGuides = FALSE, xgrid = 0, ygrid = 0
)
plotRaster(
    image = pg_type,
    x = 2.5, y = 0.25, width = 4, height = 1.5, just = "top"
)
plotRaster(
    image = gene_gnome,
    x = 2.5, y = 1, width = 3.5, height = 3.5, just = "top"
)
```

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

### Hide Page Guides

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/pageGuideHide.html

Call pageGuideHide() to remove guides from the current plotgardener page. Note: Using this function within a pdf call will render a new page with guides removed. To avoid this, set showGuides = FALSE in pageCreate.

```r
pageCreate(width = 7, height = 4, default.units = "inches")


pageGuideHide()
```

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

### Remove All Guides from the Page

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotgardener_page.html

Call `pageGuideHide()` to remove all previously added horizontal and vertical guides from the plot page.

```r
## Create page
pageCreate(width = 3, height = 3, default.units = "inches")
```

```r
## Remove guides
pageGuideHide()
```

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

### Initialize plotgardener page and load data

Source: https://github.com/phanstiellab/plotgardener/blob/devel/README.md

Loads necessary libraries and datasets, then creates a new plotgardener page with specified dimensions. This sets up the canvas for subsequent plotting.

```r
## Load libraries and datasets
library("plotgardener")
library("org.Hs.eg.db")
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("plotgardenerData")
library("AnnotationHub")
data("GM12878_HiC_10kb")
data("IMR90_HiC_10kb")
data("GM12878_ChIP_CTCF_signal")
data("IMR90_ChIP_CTCF_signal")
data("GM12878_ChIP_H3K27ac_signal")
data("IMR90_ChIP_H3K27ac_signal")

## Create a plotgardener page
pageCreate(width = 7, height = 4.25, default.units = "inches")

```

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

### Hide plotgardener Page Guides

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/introduction_to_plotgardener.html

Hides all page guides created by pageCreate(). This is typically done before exporting the plot.

```R
pageGuideHide()
```

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

### Add Specific Horizontal and Vertical Guides

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotgardener_page.html

Use `pageGuideHorizontal` and `pageGuideVertical` to add specific guide lines to the plot page after creation.

```r
pageCreate(width = 3, height = 3, default.units = "inches")
## Add a horizontal guide at y = 2.25 inches
pageGuideHorizontal(y = 2.25, default.units = "inches")
## Add a vertical guide at x = 0.75 inches
pageGuideVertical(x = 0.75, default.units = "inches")
```

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

### Hide Page Guides

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/plotRanges.html

Hides the page guides, which are typically used for layout and alignment during plot creation. This is usually called at the end of the plotting process.

```R
## Hide page guides
pageGuideHide()
```

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

### Load plotgardener and Plot Example GWAS Data

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/introduction_to_plotgardener.html

Loads the plotgardener library, necessary annotation packages, example GWAS data, and generates a quick Manhattan plot.

```R
library(plotgardener)

## Load hg19 genomic annotation packages
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

## Load example GWAS data
library(plotgardenerData)
data("hg19_insulin_GWAS")

## Quick plot GWAS data
plotManhattan(
    data = hg19_insulin_GWAS, 
    assembly = "hg19",
    fill = c("steel blue", "grey"),
    ymax = 1.1, cex = 0.20
)
```

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

### Create Plotting Page and Plot Signal Tracks

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotting_multiomic_data.html

Initialize a plotting page and then plot multiple signal tracks, ensuring they are aligned by specifying common parameters and positioning.

```R
## Create a page
pageCreate(width = 7.5, height = 2.1, default.units = "inches",
            showGuides = FALSE, xgrid = 0, ygrid = 0)

## Plot and place signal plots
signal1 <- plotSignal(
    data = IMR90_ChIP_H3K27ac_signal, params = params,
    x = 0.5, y = 0.25, width = 6.5, height = 0.65,
    just = c("left", "top"), default.units = "inches"
)

signal2 <- plotSignal(
    data = GM12878_ChIP_H3K27ac_signal, params = params,
    linecolor = "#7ecdbb",
    x = 0.5, y = 1, width = 6.5, height = 0.65,
    just = c("left", "top"), default.units = "inches"
)
```

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

### Annotate Genome Label and Hide Page Guides

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/index.html

This snippet demonstrates annotating a genome label and hiding page guides. Ensure the plot object and parameters are correctly specified.

```R
## Annotate genome label
    annoGenomeLabel(plot = genes_imr, params = params_d, 
                       scale = "Kb", fontsize = 7, digits = 0,
                       y = 3.85, just = c("right", "top"))
    ## Hide page guides
    pageGuideHide()
```

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

### Create Page and Plot Signal

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/annoHighlight.html

Initializes a plotgardener page and plots a signal track. This sets up the canvas and the primary plot before annotation.

```R
pageCreate(width = 7.5, height = 1.5, default.units = "inches")
library(plotgardenerData)
data("IMR90_ChIP_H3K27ac_signal")
region <- pgParams(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    range = c(0, 45)
)
signalPlot <- plotSignal(
    data = IMR90_ChIP_H3K27ac_signal, params = region,
    x = 0.5, y = 0.25, width = 6.5, height = 0.65,
    just = c("left", "top"),
    default.units = "inches"
)
#> signal[signal1_h]
```

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

### readCoolBpResolutions

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/readCoolBpResolutions.html

Reads basepair resolutions from a specified .mcool file.

```APIDOC
## readCoolBpResolutions

### Description
Reads basepair resolutions from an .(m)cool file.

### Arguments
#### Path Parameters
- **file** (character) - Description: A character value specifying the path to the .(m)cool file.

### Value
Vector of basepair resolutions
```

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

### Plot Genome Label

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotting_multiomic_data.html

Adds a genome label to the plot, indicating scale and chromosome. Requires chromosome, start, end, and assembly.

```R
plotGenomeLabel(
    chrom = "chr21", chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 4.5, length = 2, scale = "Mb",
    just = c("left", "top"), default.units = "inches"
)
```

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

### Plotting and Placing a Hi-C Square

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/plotHicSquare.html

This example demonstrates how to plot a Hi-C square with specified genomic regions, resolution, color range, and placement parameters. It also shows how to annotate the plot with a heatmap legend and genome labels.

```R
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create a page
pageCreate(width = 3, height = 3, default.units = "inches")

## Plot and place Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 0.5, width = 2, height = 2,
    just = c("left", "top"),
    default.units = "inches", bg = "black"
)
#> Read in dataframe.  Assuming 'chrom' in column1 and 'altchrom' in column2. 10000 BP resolution detected.
#> hicSquare[hicSquare1]

## Annotate heatmap legend
annoHeatmapLegend(
    plot = hicPlot, x = 2.6, y = 0.5,
    width = 0.12, height = 1.2,
    just = c("left", "top"), default.units = "inches"
)
#> heatmapLegend[heatmapLegend1]

## Annotate x-axis and y-axis genome labels
annoGenomeLabel(
    plot = hicPlot, scale = "Mb", axis = "x",
    x = 0.5, y = 2.53, just = c("left", "top")
)
#> genomeLabel[genomeLabel1]
annoGenomeLabel(
    plot = hicPlot, scale = "Mb", axis = "y",
    x = 0.47, y = 0.5, just = c("right", "top")
)

#> genomeLabel[genomeLabel2]

## Hide page guides
pageGuideHide()

```

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

### plotGG Function

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/plotGG.html

This snippet details the plotGG function, its parameters, and provides an example of its usage for placing a ggplot object within a plotgardener layout.

```APIDOC
## plotGG

### Description
Plot a ggplot2 plot, gtable, or grob object in a plotgardener layout.

### Signature
plotGG(
    plot,
    x,
    y,
    width,
    height,
    just = c("left", "top"),
    default.units = "inches",
    params = NULL
)

### Arguments

*   **plot** (ggplot, gtable, or grob object): The plot object to be placed.
*   **x** (numeric or unit object): The x-location for the plot.
*   **y** (numeric, unit object, or character): The y-location for the plot. Can be a character string like "b10" to place relative to the bottom of the page.
*   **width** (numeric or unit object): The width of the plot.
*   **height** (numeric or unit object): The height of the plot.
*   **just** (character vector): Justification of the plot relative to its (x, y) location. Defaults to `c("left", "top")`.
*   **default.units** (string): Default units for `x`, `y`, `width`, and `height` if specified as numerics. Defaults to "inches".
*   **params** (pgParams object, optional): Additional parameters for the plot.

### Value
Returns a `pg_gg` object containing placement and grob information.

### Example

```R
library(ggplot2)

# Create a sample ggplot object
p <- ggplot(mtcars) + geom_point(aes(mpg, disp))

# Create a plotgardener page
pageCreate(width = 4, height = 4, default.units = "inches")

# Place the ggplot object on the page
plotGG(
    plot = p,
    x = 0.5,
    y = 0.5,
    width = 3,
    height = 3,
    just = c("left", "top"),
    default.units = "inches"
)

# Add a title
plotText(label = "mtcars", fontsize = 14, fontface = "bold", x = 1, y = 0.35)

# Hide page guides
pageGuideHide()
```
```

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

### Plot Loop Annotations

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotting_multiomic_data.html

Visualizes DNA loop annotations using arches. Requires loop data, chromosome, start, end, and assembly.

```R
plotPairsArches(
    data = IMR90_DNAloops_pairs,
    chrom = "chr21", chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 2.5, width = 2, height = 0.25,
    just = c("left", "top"), default.units = "inches",
    fill = "black", linecolor = "black", flip = TRUE
)
```

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

### .coolAutoResolution

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/dot-coolAutoResolution.html

Determines the best resolution for .(m)cool files based on the size of the region.

```APIDOC
## .coolAutoResolution

### Description
Determines the best resolution for .(m)cool files based on the size of the region.

### Arguments

*   **file** (Path to .(m)cool file)
*   **chromstart** (Chromstart of region)
*   **chromend** (Chromend of region)
```

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

### Plotting a Basic Chromosome Ideogram

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/plotIdeogram.html

This snippet demonstrates how to plot a basic chromosome ideogram for a specified chromosome. Ensure the 'plotgardener' package is installed and loaded.

```R
library(plotgardener)

# Create a plotgardener page object
pag <- pageCreate()

# Plot the ideogram for chromosome 1
plotIdeogram(chrom = "chr1")

# Draw the plot\npageDraw(pag)
```

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

### Plot Signal Track Data

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/introduction_to_plotgardener.html

Quickly plot signal data using the plotSignal function. Requires loading plotgardener and example signal data.

```R
library(plotgardener)

## Load example signal data
library(plotgardenerData)
data("IMR90_ChIP_H3K27ac_signal")

## Quick plot signal data
plotSignal(
    data = IMR90_ChIP_H3K27ac_signal,
    chrom = "chr21", chromstart = 28000000, chromend = 30300000,
    assembly = "hg19"
)
```

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

### Create a plotgardener Page

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/index.html

Initialize a new plotgardener page with specified dimensions and units. This sets up the canvas for subsequent plot elements.

```R
pageCreate(width = 7, height = 4.25, default.units = "inches")
```

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

### Plot Hi-C Square Data

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/introduction_to_plotgardener.html

Quickly plot Hi-C data using the plotHicSquare function. Requires loading plotgardener and example Hi-C data.

```R
library(plotgardener)

## Load example Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Quick plot Hi-C data
plotHicSquare(
    data = IMR90_HiC_10kb,
    chrom = "chr21", chromstart = 28000000, chromend = 30300000,
    assembly = "hg19"
)
```

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

### Plot Hi-C Data

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/articles/guides/plotting_multiomic_data.html

Plots Hi-C data for a specified genomic region. Requires Hi-C data, chromosome, start, end, and assembly information.

```R
plotHicSquare(
    data = IMR90_HiC_10kb,
    chrom = "chr21", chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 0.5, width = 2, height = 2,
    just = c("left", "top"), default.units = "inches"
)
```

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

### Create Plotting Page

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/plotGenomeLabel.html

Initializes a new plotting page with specified dimensions and default units. This sets up the canvas for subsequent plotting functions.

```r
pageCreate(width = 5, height = 3, default.units = "inches")
```

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

### Load and Plot Raster Images

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/plotRaster.html

Loads PNG images using readPNG and plots them onto a plotgardener page. Demonstrates different justification options.

```R
library(png)

## Load images

pg_type <- readPNG(system.file("images",
    "pg-wordmark.png",
    package = "plotgardener"
    ))

gene_gnome <- readPNG(system.file("images",
    "pg-gnome-hole-shadow.png",
    package = "plotgardener"
    ))

rlogo <- readPNG(system.file("images", "Rlogo.png", 
                    package = "plotgardener"))

## Create page
pageCreate(width = 5, height = 6)

## Plot images
plotRaster(
    image = pg_type,
    x = 2.5, y = 0.25, width = 4, height = 1.5,
    just = "top"
    )

plotRaster(
    image = gene_gnome,
    x = 2.5, y = 2.25, width = 3.5, height = 3.5,
    just = "top"
    )

plotRaster(
    image = rlogo,
    x = 1, y = 1.5, width = 0.5, height = 0.45,
    just = c("left", "top")
    )

## Hide page guies
pageGuideHide()
```

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

### Plot Genome Label

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/annoHighlight.html

Plots a label for a specified genomic region. Allows customization of chromosome, start and end positions, assembly, and plot dimensions.

```APIDOC
## plotGenomeLabel

### Description
Plots a label for a specified genomic region.

### Parameters
- **chrom** (string) - The chromosome to plot.
- **chromstart** (numeric) - The starting position on the chromosome.
- **chromend** (numeric) - The ending position on the chromosome.
- **assembly** (string) - The genome assembly (e.g., "hg19").
- **x** (numeric) - The x-coordinate for the label.
- **y** (numeric) - The y-coordinate for the label.
- **length** (numeric) - The length of the label.
- **default.units** (string) - The default units for length (e.g., "inches").

### Returns
#> genomeLabel[genomeLabel1]
```

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

### Plot Genome Label

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/annoHighlight.html

Plots a label for a specific genomic region. Specify the chromosome, start and end coordinates, assembly, and desired position and size.

```r
plotGenomeLabel(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 1.3, length = 6.5, default.units = "inches"
)
```

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

### assembly()

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/reference/index.html

Make an `assembly` object for alternate TxDb, OrgDb, and BSgenome genomic annotation packages.

```APIDOC
## assembly()

### Description
Make an `assembly` object for alternate TxDb, OrgDb, and BSgenome genomic annotation packages.

### Method
Function Call

### Endpoint
N/A (R function)

### Parameters
* **genome**: The name of the genome assembly.
* **...**: Additional arguments for specifying annotation packages.
```

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

### Define plotgardener Parameters

Source: https://github.com/phanstiellab/plotgardener/blob/devel/docs/index.html

Set genomic and dimension parameters for a plot using the `pgParams` function. This specifies the chromosome, start, and end coordinates for the visualization.

```R
params_a <- pgParams(chrom = "chr21", chromstart = 28000000, chromend = 30300000)
```