Plotgardener

https://phanstiellab.github.io/plotgardener/
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Plotgardener is a genomic data visualization package for R that enables users to programmatically...
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### Full Example: Create, Plot, Hide, and Show Page Guides

Source: https://phanstiellab.github.io/plotgardener/reference/pageGuideShow.html

This example demonstrates the complete workflow of creating a page, adding guides, plotting data, hiding guides, and then showing them again. It requires loading the `plotgardenerData` package and sample data.

```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")
)
```

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

### Create Custom Assembly Object

Source: https://phanstiellab.github.io/plotgardener/reference/assembly.html

Example of creating a custom `assembly` object for hg38/GRCh38. Ensure the specified annotation packages are installed.

```R
## Create a custom `assembly` object for hg38/GRCh38 packages
newAssembly <- assembly(
    Genome = "hg38_GRCh38",
    TxDb = "TxDb.Hsapiens.UCSC.hg38.knownGene",
    OrgDb = "org.Hs.eg.db",
    BSgenome = "BSgenome.Hsapiens.NCBI.GRCh38"
)
```

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

### Example: Plotting Paired Ranges with Customization

Source: https://phanstiellab.github.io/plotgardener/reference/plotPairs.html

This example demonstrates how to load paired ranges data, set plotting parameters including chromosome, start, end, and assembly, create a plotgardener page, and add a length column to the data before plotting.

```R
## Load paired ranges data in BEDPE format
library(plotgardenerData)
data("IMR90_DNAloops_pairs")

## Set the coordinates
params <- pgParams(
    chrom = "chr21",
    chromstart = 27900000, chromend = 30700000,
    assembly = "hg19",
    width = 7
)

## Create a page
pageCreate(width = 7.5, height = 2.1, default.units = "inches")

## Add a length column
IMR90_DNAloops_pairs$length <- 
        (IMR90_DNAloops_pairs$start2 - IMR90_DNAloops_pairs$start1) / 1000
```

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

### Show Page Guides

Source: https://phanstiellab.github.io/plotgardener/reference/pageGuideShow.html

Use `pageGuideShow()` to re-display guides that have been hidden. This function does not take any arguments.

```R
pageGuideShow()
```

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

### Example: Plotting Multiple Signal Tracks

Source: https://phanstiellab.github.io/plotgardener/reference/plotSignal.html

This example demonstrates loading signal data, creating a page, defining a genomic region, and plotting two different signal tracks with associated labels and genome information. It also includes hiding page guides.

```R
## Load signal data
library(plotgardenerData)
data("IMR90_ChIP_H3K27ac_signal")
data("GM12878_ChIP_H3K27ac_signal")

## Create a page
pageCreate(width = 7.5, height = 2.1, default.units = "inches")

## Define region
region <- pgParams(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    range = c(0, 45)
)

## Plot and place signal plots
signal1 <- 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]

signal2 <- plotSignal(
    data = GM12878_ChIP_H3K27ac_signal, params = region,
    linecolor = "#7ecdbb",
    x = 0.5, y = 1, width = 6.5, height = 0.65,
    just = c("left", "top"), default.units = "inches"
)
#> signal[signal2_h]

## Plot genome label
plotGenomeLabel(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 1.68, length = 6.5,
    default.units = "inches"
)
#> genomeLabel[genomeLabel1]

## Add text labels
plotText(
    label = "IMR90", fonsize = 10, fontcolor = "#37a7db",
    x = 0.5, y = 0.25, just = c("left", "top"),
    default.units = "inches"
)
#> text[text1]
plotText(
    label = "GM12878", fonsize = 10, fontcolor = "#7ecdbb",
    x = 0.5, y = 1, just = c("left", "top"),
    default.units = "inches"
)

#> text[text2]

## Hide page guides
pageGuideHide()

```

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

### Read .cool file example

Source: https://phanstiellab.github.io/plotgardener/reference/readCool.html

Demonstrates reading a .cool file for a specific region and resolution. Ensure the file is downloaded before reading.

```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.
```

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

### Add Specific Horizontal and Vertical Guides

Source: https://phanstiellab.github.io/plotgardener/articles/guides/plotgardener_page.html

Illustrates adding precise horizontal and vertical guides to a page using `pageGuideHorizontal()` and `pageGuideVertical()` after creating the page with `pageCreate()`.

```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")
```

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

### Read .mcool file example (100Kb resolution)

Source: https://phanstiellab.github.io/plotgardener/reference/readCool.html

Demonstrates reading a .mcool file for a specific region and 100Kb resolution. Ensure the file is downloaded before reading.

```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.
```

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

### Load Hi-C Data Example

Source: https://phanstiellab.github.io/plotgardener/reference/plotHicRectangle.html

This example demonstrates how to load Hi-C data using the plotgardenerData package. It is a prerequisite for plotting Hi-C matrices.

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

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

### Example: Plotting Chromosome 2 Ideogram with Annotations

Source: https://phanstiellab.github.io/plotgardener/reference/plotIdeogram.html

Demonstrates loading necessary libraries, creating a plot page, plotting an ideogram for 'chr2' with specific placement and dimensions, and adding a text label. Hides page guides at the end.

```R
## Load Giemsa stain band information and genomic
## annotation data for hg19 genome assembly
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(AnnotationHub)
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr
#> 
#> Attaching package: ‘AnnotationHub’
#> The following object is masked from ‘package:rtracklayer’:
#> 
#>     hubUrl
#> The following object is masked from ‘package:Biobase’:
#> 
#>     cache

## Create page
pageCreate(width = 4.5, height = 1, default.units = "inches")

## Plot and place ideogram
ideogramPlot <- plotIdeogram(
    chrom = "chr2", assembly = "hg19",
    x = 0.25, y = 0.25, width = 4, height = 0.3,
    just = c("left", "top"),
    default.units = "inches"
)
#> ideogram[ideogram1]

## Plot text
plotText(
    label = "Chromosome 2", fontcolor = "dark grey",
    x = 4.25, y = 0.65, just = "right"
)

#> text[text1]

## Hide page guides
pageGuideHide()
```

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

### Read .mcool file example (2500Kb resolution)

Source: https://phanstiellab.github.io/plotgardener/reference/readCool.html

Demonstrates reading a .mcool file for a specific chromosome at a 2500Kb resolution. Ensure the file is downloaded before reading.

```R
## Read in data for chr2 at 2500Kb resolution 
mcoolData_2500Kb <- readCool(file = mcoolFile, chrom = "2",
                             resolution = 2500000)
#> Read in .mcool file with NONE normalization at 2500000 BP resolution.
```

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

### Example: Load annotation and create page

Source: https://phanstiellab.github.io/plotgardener/reference/plotGenes.html

Loads necessary genomic annotation packages (TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db) and initializes a plotgardener page for plotting.

```R
## Load hg19 genomic annotation packages
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("org.Hs.eg.db")

## Set genomic coordinates
paramssmall <- pgParams(
    chrom = "chr8",
    chromstart = 1, chromend = 3000000,
    assembly = "hg19", width = 7
)
paramsbig <- pgParams(
    chrom = "chr8",
    chromstart = 1, chromend = 146364022,
    assembly = "hg19", width = 7
)
## Set colors
cols <- c("#41B6C4", "#225EA8")

## Create page
pageCreate(width = 7.5, height = 3.5, default.units = "inches")
```

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

### Example: Plotting and Annotating Ranges Data

Source: https://phanstiellab.github.io/plotgardener/reference/plotRanges.html

This example demonstrates loading ranges data, creating a plot page, plotting a pileup ranges plot with strand information, annotating it with a genome label, and adding text labels for strands. Ensure plotgardenerData is loaded.

```R
## Load ranges data in BED format
library(plotgardenerData)
data("IMR90_ChIP_CTCF_reads")

## Create page
pageCreate(width = 7.5, height = 5, default.units = "inches")

## Plot and place a pileup ranges plot
pileupPlot <- plotRanges(
    data = IMR90_ChIP_CTCF_reads, chrom = "chr21",
    chromstart = 29073000, chromend = 29074000,
    assembly = "hg19",
    order = "random",
    fill = colorby("strand", palette = 
                colorRampPalette(c("#7ecdbb", "#37a7db"))),
    strandSplit = TRUE, 
    x = 0.5, y = 0.25, width = 6.5, height = 4.25,
    just = c("left", "top"), default.units = "inches"
)
#> Warning: Not enough plotting space for all provided elements. ('+' indicates elements not shown.)
#> Warning: Not enough plotting space for all provided elements. ('+' indicates elements not shown.)
#> ranges[ranges1]

## Annotate genome label
annoGenomeLabel(
    plot = pileupPlot, x = 0.5, y = 4.5,
    just = c("left", "top")
)
#> genomeLabel[genomeLabel1]

## Add text labels
plotText(
    label = "+ strand", fontcolor = "#37a7db", fontsize = 12,
    x = 0.5, y = 1.25, just = "left"
)
#> text[text1]
plotText(
    label = "- strand", fontcolor = "#7ecdbb", fontsize = 12,
    x = 0.5, y = 3.5, just = "left"
)

#> text[text2]

## Hide page guides
pageGuideHide()
```

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

### Create a 6x4.5 Inch Page

Source: https://phanstiellab.github.io/plotgardener/reference/pageCreate.html

Example of creating a page with specified width and height in inches.

```R
pageCreate(width = 6, height = 4.5, default.units = "inches")
```

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

### Plot and annotate Hi-C data with domains

Source: https://phanstiellab.github.io/plotgardener/reference/annoDomains.html

This example demonstrates loading Hi-C data, creating a square Hi-C plot, and then annotating specific genomic domains on the bottom half of the plot with a red line color. It also includes annotations for a heatmap legend and genome label, and hides page guides.

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

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

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"
)

annoDomains(
    plot = hicPlot, data = domains,
    half = "bottom", linecolor = "red"
)

annoHeatmapLegend(
    plot = hicPlot,
    x = 3.6, y = 0.5, width = 0.12, height = 1.2,
    just = c("left", "top"), default.units = "inches"
)

annoGenomeLabel(
    plot = hicPlot, x = 0.5, y = 3.53, scale = "Mb",
    just = c("left", "top")
)

pageGuideHide()
```

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

### Create a 14x10 cm Page

Source: https://phanstiellab.github.io/plotgardener/reference/pageCreate.html

Example of creating a page with specified width and height in centimeters.

```R
pageCreate(width = 14, height = 10, default.units = "cm")
```

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

### Basic plotPairsArches Example

Source: https://phanstiellab.github.io/plotgardener/reference/plotPairsArches.html

This example demonstrates how to load paired ranges data, set plotting parameters, create a page, and add an annotated pair arches plot.

```R
## Load paired ranges data in BEDPE format
library(plotgardenerData)
data("IMR90_DNAloops_pairs")

## Set the coordinates
params <- pgParams(
    chrom = "chr21",
    chromstart = 27900000, chromend = 30700000,
    assembly = "hg19",
    width = 7
)

## Create a page
pageCreate(width = 7.5, height = 2.1, default.units = "inches")

## Add a length column to color by
IMR90_DNAloops_pairs$length <- 
        (IMR90_DNAloops_pairs$start2 - IMR90_DNAloops_pairs$start1) / 1000

## Translate lengths into heights
IMR90_DNAloops_pairs$h <- 
        IMR90_DNAloops_pairs$length / max(IMR90_DNAloops_pairs$length)

## Plot the data
archPlot <- plotPairsArches(
    data = IMR90_DNAloops_pairs, params = params,
    fill = colorby("length", palette = 
                colorRampPalette(c("dodgerblue2", "firebrick2"))),
    linecolor = "fill",
    archHeight = "h", alpha = 1,
    x = 0.25, y = 0.25, height = 1.5,
    just = c("left", "top"),
    default.units = "inches"
)
#> arches[arches1]

## Annotate genome label
annoGenomeLabel(plot = archPlot, x = 0.25, y = 1.78, scale = "Mb")
#> genomeLabel[genomeLabel1]


## Annotate heatmap legend
annoHeatmapLegend(
    plot = archPlot, fontcolor = "black",
    x = 7.0, y = 0.25,
    width = 0.10, height = 1, fontsize = 10
)
#> heatmapLegend[heatmapLegend1]

## Add the heatmap legend title
plotText(
    label = "Kb", rot = 90, x = 6.9, y = 0.75,
    just = c("center", "center"),
    fontsize = 10
)

#> text[text1]


## Hide page guides
pageGuideHide()
```

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

### Example: Plotting Transcripts with PlotGardener

Source: https://phanstiellab.github.io/plotgardener/reference/plotTranscripts.html

Demonstrates loading annotation packages, creating a page, and plotting transcripts with placement, genome labels, and a legend. Requires TxDb and org.Hs.eg.db packages.

```R
## Load hg19 genomic annotation packages
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("org.Hs.eg.db")

## Create page
pageCreate(width = 7.5, height = 3.5, default.units = "inches")

## Plot and place transcripts
plotTranscripts(
    chrom = "chr8", chromstart = 1000000, chromend = 2000000,
    assembly = "hg19", labels = "gene",
    x = 0.5, y = 0.5, width = 6.5, height = 2.5,
    just = c("left", "top"), default.units = "inches"
)
#> Warning: Not enough plotting space for all provided elements. ('+' indicates elements not shown.)
#> transcripts[transcripts1]

## Plot genome label
plotGenomeLabel(
    chrom = "chr8", chromstart = 1000000, chromend = 2000000,
    assembly = "hg19",
    x = 0.5, y = 3.03, length = 6.5, default.units = "inches"
)
#> genomeLabel[genomeLabel1]

## Plot a legend
plotLegend(
    legend = c("+ strand", "- strand"),
    fill = c("#669fd9", "#abcc8e"), border = FALSE,
    x = 0.5, y = 1, width = 1, height = 0.5,
    just = c("left", "top")
)

#> legend[legend1]

## Hide page guides
pageGuideHide()
```

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

### Remove All Guides from the Page

Source: https://phanstiellab.github.io/plotgardener/articles/guides/plotgardener_page.html

Demonstrates how to remove all previously added guides from the plot using the `pageGuideHide()` function.

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

```R
## Remove guides
pageGuideHide()
```

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

### Load Hi-C Data and Create Page

Source: https://phanstiellab.github.io/plotgardener/reference/plotHicTriangle.html

This example demonstrates loading Hi-C data using plotgardenerData and setting up a plotting page using pageCreate. This is a prerequisite for plotting Hi-C triangles.

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

## Create a page
pageCreate(width = 4, height = 2.5, default.units = "inches")
```

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

### Install plotgardener and plotgardenerData

Source: https://phanstiellab.github.io/plotgardener/index.html

Installs the plotgardener package and its associated data package from Bioconductor. Ensure you have the correct R and Bioconductor versions.

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

BiocManager::install(version = "3.19")

BiocManager::install("plotgardener")
```

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

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

### Quick Plotting with plotHicSquare

Source: https://phanstiellab.github.io/plotgardener/reference/plotHicSquare.html

An example of using plotHicSquare for quick plotting by ignoring plot placement parameters.

```APIDOC
## plotHicSquare (Quick Plot)

### Description
This function can be used to quickly plot an unannotated square Hi-C plot by ignoring plot placement parameters.

### Parameters
- **data**: Hi-C data object.
- **chrom**: Chromosome to plot.
- **chromstart** (numeric, optional): Start position of the chromosome region.
- **chromend** (numeric, optional): End position of the chromosome region.
```

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

### Inspect BED Data with head()

Source: https://phanstiellab.github.io/plotgardener/articles/guides/plotgardener_meta_functions.html

Use `data()` to load sample BED data and `head()` to inspect the first few rows, including columns like 'chrom', 'start', 'end', and 'strand'.

```R
data("IMR90_ChIP_CTCF_reads")
head(IMR90_ChIP_CTCF_reads)
#>          chrom    start      end strand
#> 15554862 chr21 28000052 28000088      -
#> 15554863 chr21 28000092 28000128      -
#> 15554864 chr21 28000162 28000198      -
#> 15554865 chr21 28000251 28000287      +
#> 15554866 chr21 28000335 28000371      -
#> 15554867 chr21 28000500 28000536      +
```

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

### pageGuideHide

Source: https://phanstiellab.github.io/plotgardener/reference/pageGuideHide.html

Removes guides from the current plotgardener page. Note that using this within a pdf call may result in a new page being rendered.

```APIDOC
## Function: pageGuideHide

### Description
Removes guides from the current plotgardener page.

### Usage
```R
pageGuideHide()
```

### Details
When used within a `pdf` call, `pageGuideHide` can cause a new page to be rendered with guides removed. To avoid this, use `showGuides = FALSE` in the `pageCreate` function.

### Value
None.

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

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

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

### Quick Plot Hi-C Data with plotgardener

Source: https://phanstiellab.github.io/plotgardener/articles/introduction_to_plotgardener.html

Loads plotgardener and example Hi-C data, then quickly plots a Hi-C square. This method omits placement arguments for rapid data inspection.

```R
library(plotgardener)

library(plotgardenerData)
data("IMR90_HiC_10kb")

plotHicSquare(
    data = IMR90_HiC_10kb,
    chrom = "chr21", chromstart = 28000000, chromend = 30300000,
    assembly = "hg19"
)
```

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

### Get Default Packages for a Genome with defaultPackages()

Source: https://phanstiellab.github.io/plotgardener/articles/guides/plotgardener_meta_functions.html

Use `defaultPackages()` with a genome name (e.g., 'hg19') to retrieve associated annotation packages like TxDb, OrgDb, and BSgenome.

```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"
```

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

### Create and Add a Legend to a Plot

Source: https://phanstiellab.github.io/plotgardener/reference/plotLegend.html

This example demonstrates how to create a legend with specified text and fill colors, and then add it to a plot. It requires loading the plotgardenerData library and creating a plot page first.

```R
## Load BED data
library(plotgardenerData)
data("IMR90_ChIP_CTCF_reads")

## Create page
pageCreate(width = 7.5, height = 4, default.units = "inches")

## Plot a pileup plot, coloring elements by strand
pileupPlot <- plotRanges(
    data = IMR90_ChIP_CTCF_reads, chrom = "chr21",
    chromstart = 29072500, chromend = 29075000,
    assembly = "hg19",
    fill = colorby("strand", palette = 
                colorRampPalette(c("steel blue", "light salmon"))),
    x = 0.5, y = 3.5, width = 6.5, height = 3.5,
    just = c("left", "bottom"),
    default.units = "inches"
)
#> Warning: Not enough plotting space for all provided elements. ('+' indicates elements not shown.)
#> ranges[ranges1]

## Add a legend depicting strand colors
legendPlot <- plotLegend(
    legend = c("- strand", "+ strand"),
    fill = c("steel blue", "light salmon"),
    border = FALSE,
    x = 5, y = 0.5, width = 1.5, height = 0.7,
    just = c("left", "top"),
    default.units = "inches"
)
#> legend[legend1]

## Annotate genome label
annoGenomeLabel(
    plot = pileupPlot, x = 0.5, y = 3.5,
    just = c("left", "top")
)

#> genomeLabel[genomeLabel1]

## Hide page guides
pageGuideHide()
```

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

### Create a Standard 8.5 x 11 Inch Page

Source: https://phanstiellab.github.io/plotgardener/articles/guides/plotgardener_page.html

Use `pageCreate()` to set up a page with specified width, height, and default units. Gridlines are set to 0.5 by default.

```R
pageCreate(width = 8.5, height = 11, default.units = "inches")
```

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

### Hide Plot Guides

Source: https://phanstiellab.github.io/plotgardener/articles/introduction_to_plotgardener.html

Hide the guides on a plotgardener page. This function is typically called before exporting the plot.

```R
pageGuideHide()
```

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

### Hide Page Guides

Source: https://phanstiellab.github.io/plotgardener/reference/plotPolygon.html

A utility function to hide guides on the plotgardener page, typically used after plotting is complete.

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

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

### Hide Page Guides - plotgardener

Source: https://phanstiellab.github.io/plotgardener/reference/pageGuideHide.html

Use pageGuideHide() to remove guides from the current page. Avoid using within pdf calls; use showGuides = FALSE in pageCreate instead.

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


pageGuideHide()
```

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

### Create a Page

Source: https://phanstiellab.github.io/plotgardener/reference/plotHicRectangle.html

Initializes a new page for plotting with specified dimensions and units.

```r
pageCreate(width = 6, height = 3.5, default.units = "inches")
```

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

### Load Data and Create Page

Source: https://phanstiellab.github.io/plotgardener/reference/annoPixels.html

Loads necessary Hi-C and BEDPE data and initializes a plotting page. Requires the plotgardenerData package.

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

pageCreate(width = 4.5, height = 4, default.units = "inches")
```

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

### Create a Page Layout

Source: https://phanstiellab.github.io/plotgardener/articles/guides/incorporating_ggplots.html

Initializes a new page with specified dimensions and units. This serves as the canvas for arranging plots.

```R
pageCreate(width = 9.5, height = 3.5, default.units = "inches")
```

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

### annoSegments Function

Source: https://phanstiellab.github.io/plotgardener/reference/annoSegments.html

Annotates a line segment within a plot by drawing a line between specified start and end points.

```APIDOC
## annoSegments

### Description
Annotates a line segment within a plot.

### Arguments
- **x0** (numeric vector or unit object) - Starting x-values of the line segments.
- **y0** (numeric vector or unit object) - Starting y-values of the line segments.
- **x1** (numeric vector or unit object) - Stopping x-values of the line segments.
- **y1** (numeric vector or unit object) - Stopping y-values of the line segments.
- **plot** (plotgardener plot) - The plot to draw the segments on.
- **default.units** (string) - Default units for numeric vectors. Default is "native".
- **linecolor** (string) - Color of the line segment. Default is "black".
- **lwd** (numeric) - Width of the line segment. Default is 1.
- **lty** (numeric) - Type of the line segment. Default is 1.
- **lineend** (string) - Style of the line segment ends. Options: "round", "butt", "square". Default is "butt".
- **linejoin** (string) - Style of the line segment joins. Options: "round", "mitre", "bevel". Default is "mitre".
- **arrow** (list) - Arrow head specifications.
- **params** (pgParams object) - Optional parameters.
- **...** - Additional graphical parameters.

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

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

### Inspect bigWig data structure

Source: https://phanstiellab.github.io/plotgardener/articles/guides/reading_data_for_plotgardener.html

The output of readBigwig() contains seqnames, start, end, width, strand, and score columns.

```R
head(bwRegion)
```

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

### Full Example: Plotting and Annotating a Hi-C Square

Source: https://phanstiellab.github.io/plotgardener/reference/plotHicSquare.html

Demonstrates loading Hi-C data, creating a plotgardener page, plotting a Hi-C square with specified parameters, and adding annotations like a heatmap legend and genome labels. Requires the plotgardenerData package.

```R
## Load Hi-C data
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()
```

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

### Create and Place Hi-C Plot on Page

Source: https://phanstiellab.github.io/plotgardener/reference/pagePlotPlace.html

Demonstrates loading data, creating a Hi-C plot without drawing it, initializing a plotgardener page, and then placing the created Hi-C plot onto the page with specified dimensions and position. Also shows annotation of a heatmap legend and hiding page guides.

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

## Create, but do not plot, square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    draw = FALSE
)
#> Read in dataframe.  Assuming 'chrom' in column1 and 'altchrom' in column2. 10000 BP resolution detected.
#> hicSquare[hicSquare1]

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

## Place Hi-C plot on page
pagePlotPlace(
    plot = hicPlot,
    x = 0.25, y = 0.25, width = 3, height = 3,
    just = c("left", "top"),
    default.units = "inches", draw = TRUE
)
#> hicSquare[hicSquare1]

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

#> heatmapLegend[heatmapLegend1]

## Hide page guides
pageGuideHide()
```

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

### Create a Custom Sized Page with Gridlines

Source: https://phanstiellab.github.io/plotgardener/articles/guides/plotgardener_page.html

Demonstrates creating a page with custom dimensions (8x8 cm) and gridlines (1 unit) using `pageCreate()`.

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

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

### Read All Chr22 Data

Source: https://phanstiellab.github.io/plotgardener/reference/readHic.html

Reads Hi-C data for the entire chromosome 22 at a specified resolution (2.5Mb). Ensure the 'plotgardenerData' package is installed for system.file.

```R
hicFile <- system.file("extdata/test_chr22.hic", package="plotgardenerData")

## Read in data for all chr22 file at 2.5Mb bp resolution
hicData <- readHic(file = hicFile, chrom = "22",
                    assembly = "hg19",
                    resolution = 2500000) 
#> Read in hic file with KR normalization at 2500000 BP resolution.
                        
```

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

### readCoolBpResolutions

Source: https://phanstiellab.github.io/plotgardener/reference/readCoolBpResolutions.html

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

```APIDOC
## readCoolBpResolutions

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

### Arguments
* **file** (character) - The path to the .(m)cool file.

### Value
Vector of basepair resolutions.
```

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

### Read Normalizations from .mcool File

Source: https://phanstiellab.github.io/plotgardener/reference/readCoolNorms.html

Use this function to get a list of available normalization types from a .mcool file. Optionally specify resolutions to read from.

```R
readCoolNorms(file, resolution = NULL)
```

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

### Load Genomic Annotation Packages and Create Page

Source: https://phanstiellab.github.io/plotgardener/reference/plotGenomeLabel.html

Before plotting, load necessary genomic annotation packages like TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, and BSgenome.Hsapiens.UCSC.hg19. Then, create a plotgardener page with specified dimensions.

```R
## Load hg19 genomic annotation packages
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("org.Hs.eg.db")
library("BSgenome.Hsapiens.UCSC.hg19")
#> Loading required package: BSgenome
#> Loading required package: Biostrings
#> Loading required package: XVector
#> 
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:grid’:
#> 
#>     pattern
#> The following object is masked from ‘package:base’:
#> 
#>     strsplit
#> Loading required package: BiocIO
#> Loading required package: rtracklayer

## Create page
pageCreate(width = 5, height = 3, default.units = "inches")
```

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

### Integrate ComplexHeatmap into plotgardener Layout

Source: https://phanstiellab.github.io/plotgardener/articles/guides/incorporating_ggplots.html

Embeds a captured ComplexHeatmap object into a plotgardener figure. This example also plots HiC, ChIP-seq signal, genes, and annotations.

```R
data("GM12878_HiC_10kb")
data("GM12878_ChIP_CTCF_signal")
data("GM12878_ChIP_H3K27ac_signal")
library("org.Hs.eg.db")
library("TxDb.Hsapiens.UCSC.hg19.knownGene")

## Create page
pageCreate(
    width = 6, height = 4, default.units = "inches")

params <- pgParams(chrom = "chr21", chromstart = 28150000, chromend = 29150000, 
                   assembly = "hg19",
                   x = 0.5, width = 2, default.units = "inches")
ctcf_range <- pgParams(range = c(0, 77),
                       assembly = "hg19")
hk_range <- pgParams(range = c(0, 32.6),
                     assembly = "hg19")
hic_gm <- plotHicTriangle(data = GM12878_HiC_10kb, params = params,
                          zrange = c(0, 200), resolution = 10000,
                          y = 1.5, height = 1.25, just = c("left", "bottom"))
annoHeatmapLegend(plot = hic_gm, fontsize = 7, 
                  x = 2.5, y = 0.5, width = 0.07, height = 0.5, 
                  just = c("right", "top"), default.units = "inches")
ctcf_gm <- plotSignal(data = GM12878_ChIP_CTCF_signal, params = c(params, ctcf_range),
                      fill = "#253494", linecolor = "#253494",
                      y = 1.6, height = 0.6)
plotText(label = "CTCF", fontcolor = "#253494", fontsize = 8,
         x = 0.5, y = 1.6, just = c("left","top"), default.units = "inches")
hk_gm <- plotSignal(data = GM12878_ChIP_H3K27ac_signal, params = c(params, hk_range),
                    fill = "#37a7db", linecolor = "#37a7db",
                    y = 2.3, height = 0.6, just = c("left", "top"))
plotText(label = "H3K27ac", fontcolor = "#37a7db", fontsize = 8,
         x = 0.5, y = 2.4, just = c("left","bottom"), default.units = "inches")
genes_gm <- plotGenes(params = params, stroke = 1, fontsize = 6,
                      strandLabels = FALSE,
                      y = 3, height = 0.4)
annoGenomeLabel(plot = genes_gm, params = params, 
                scale = "Kb", fontsize = 7,
                y = 3.5, digits = 0)

## Add ComplexHeatmap
gg_heatmap <- plotGG(
    plot = heatmap,
    x = 3, y = 0.5,
    width = 2.5, height = 3
)
seekViewport(name = "heatmap_matrix_2")
grid.xaxis(at = c(0, 0.5, 1), label = FALSE, gp = gpar(lwd = 0.5))
seekViewport(name = "page")

plotText(label = "Simulated Data", x = 4.25, y = 0.5,
         fontsize = 12, just = "bottom")
plotText(label = c(-2, 0, 2), x = c(3.065, 4.255, 5.425), 
         y = 3.6, fontsize = 7)
plotText(label = "Distance from center", x = 4.25, 
         y = 3.75, fontsize = 8)

## Hide page guides
pageGuideHide()
```

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

### Create a Page and Plot Complex Polygons

Source: https://phanstiellab.github.io/plotgardener/reference/plotPolygon.html

Demonstrates creating a plotgardener page and then plotting two distinct complex polygons with specified fill colors and no outlines.

```R
## Create a page
pageCreate(width = 7.5, height = 6, default.units = "inches")

## Plot complex polygons one at a time
plotPolygon(
    x = c(2.6, 4.65, 4.75, 6.05, 1.4, 1.3),
    y = c(2.5, 3.1, 3.5, 4, 3.15, 2.8),
    fill = "#4a168e", linecolor = NA
)
#>
#> polygon[polygon1]

plotPolygon(
    x = c(4.65, 4.75, 6.05, 5.05, 4.4),
    y = c(3.1, 3.5, 4, 1.45, 1.2),
    fill = "#9d28b0", linecolor = NA
)
#>
#> polygon[polygon2]
```

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

### Plot Genome Label

Source: https://phanstiellab.github.io/plotgardener/articles/guides/plotting_multiomic_data.html

Use plotGenomeLabel to add a visual representation of a genomic region to your plot. Specify chromosome, start and end coordinates, assembly, and positioning.

```R
plotGenomeLabel(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 1.68, length = 6.5,
    default.units = "inches"
)
```

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

### Display Session Information

Source: https://phanstiellab.github.io/plotgardener/articles/introduction_to_plotgardener.html

Show the R version, platform, locale, and attached packages. Useful for reproducibility.

```R
sessionInfo()
```

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

### Define GRanges object for TAD ranges

Source: https://phanstiellab.github.io/plotgardener/reference/annoDomains.html

Create a GRanges object to specify the start and end coordinates of genomic domains for annotation. Requires the GenomicRanges library.

```R
library(GenomicRanges)
library(IRanges)
domains <- GRanges("chr21",
    ranges = IRanges(
        start = c(28210000, 29085000, 29430000, 29700000),
        end = c(29085000, 29430000, 29700000, 30125000)
    )
)
```

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

### Create a Plotgardener Page

Source: https://phanstiellab.github.io/plotgardener/articles/introduction_to_plotgardener.html

Initialize a new plotting page with specified dimensions and units. This is the first step in building a plotgardener figure.

```R
pageCreate(width = 3.25, height = 3.25, default.units = "inches")
```

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

### Plot Genome Label at Mb Scale

Source: https://phanstiellab.github.io/plotgardener/reference/plotGenomeLabel.html

Plots a genome label for a specified chromosome region at the megabase (Mb) scale. Ensure the 'plotgardener' package is installed and loaded.

```R
plotGenomeLabel(
    chrom = "chr8",
    chromstart = 1000000, chromend = 2000000,
    assembly = "hg19",
    scale = "Mb",
    x = 0.5, y = 1.25, length = 4, just = c("left", "top"),
    default.units = "inches"
)
```

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

### Create a Page with Gridlines Disabled

Source: https://phanstiellab.github.io/plotgardener/articles/guides/plotgardener_page.html

Shows how to turn off gridlines entirely by setting `xgrid` and `ygrid` to 0 in `pageCreate()`.

```R
pageCreate(
    width = 3, height = 3, xgrid = 0, ygrid = 0,
    default.units = "inches"
)
```
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