> For the complete documentation index, see [llms.txt](https://www.microbiomestat.wiki/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://www.microbiomestat.wiki/data-manipulation-and-transformation/color-palette.md).

# Color Palette

## Custom Color Palette Retrieval

### mStat\_get\_palette Function

Choosing the right color palette is essential for creating visually appealing and informative data visualizations. The `mStat_get_palette()` function in MicrobiomeStat allows users to easily access and utilize a variety of color palettes, especially those inspired by and sourced from the scientific publication realm, through the `ggsci` package.

#### Overview

`mStat_get_palette()` is tailored for users who need predefined or custom color palettes for their data visualizations in R. It offers an extensive selection from the `ggsci` package, known for its scientific journal-inspired palettes, as well as the flexibility to specify custom color sets.

**Functionality:**

* Access predefined palettes like 'npg', 'aaas', 'nejm', 'lancet', 'jama', 'jco', and 'ucscgb' from the `ggsci` package.
* Provide a vector of custom color codes.
* Return a default palette in case of `NULL` input or unrecognized palette names.

#### Usage

```r
# Default palette
mStat_get_palette()

# Predefined `ggsci` palette: 'nejm'
mStat_get_palette("nejm")

# Custom color vector
mStat_get_palette(c("#123456", "#654321"))
```

#### Parameters

* `palette`: A character string for predefined palettes or a vector of color codes. If `NULL` or unrecognized, a default palette is used.

#### Details

Here's a glimpse into the functioning of `mStat_get_palette()`:

* It first checks if the `palette` parameter is `NULL`, a character string, or a vector.
* For a character string, it verifies if the name matches one of the predefined palettes in the `ggsci` database.
* If a match is found, the corresponding palette is returned.
* For a vector input, the vector itself is returned as the palette.
* In case of `NULL` or an unrecognized input, a default set of colors is provided.

#### Applications

This function is highly beneficial for:

* Enhancing the visual appeal of data plots in scientific publications.
* Customizing color schemes to match specific publication or presentation themes.
* Ensuring consistency and accuracy of color representation in multiple visualizations.

#### Visual Representation

* npg

<figure><img src="https://3375851868-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhFAmY4z7d1R15Cv49vXQ%2Fuploads%2F0P1uwvzksQA6XZzBPQcP%2FScreenshot%202024-01-10%20at%2015.26.49.png?alt=media&amp;token=54aceda4-ab4c-4af2-934e-d33a14ad6509" alt=""><figcaption></figcaption></figure>

* lancet

<figure><img src="https://3375851868-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhFAmY4z7d1R15Cv49vXQ%2Fuploads%2FxONmpQiHNtqzBa8qTRJz%2FScreenshot%202024-01-10%20at%2015.27.24.png?alt=media&amp;token=ebc71dd7-d18b-4ae4-b324-c1f3a3d23ff4" alt=""><figcaption></figcaption></figure>

* aaas

<figure><img src="https://3375851868-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhFAmY4z7d1R15Cv49vXQ%2Fuploads%2F0bEYMWrUQUkVktUiIPIW%2FScreenshot%202024-01-10%20at%2015.27.06.png?alt=media&amp;token=9ba4550c-a14b-42a1-8e6a-95719e0ac9f1" alt=""><figcaption></figcaption></figure>

* nejm

<figure><img src="https://3375851868-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhFAmY4z7d1R15Cv49vXQ%2Fuploads%2FuS6KmJWD6kmiyYCHRLBW%2FScreenshot%202024-01-10%20at%2015.28.02.png?alt=media&amp;token=a6848143-d17b-4246-bf28-19c7cefbc33b" alt=""><figcaption></figcaption></figure>

* jama

<figure><img src="https://3375851868-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhFAmY4z7d1R15Cv49vXQ%2Fuploads%2FUXvNbh4WD9eF9BPalVbO%2FScreenshot%202024-01-10%20at%2015.28.41.png?alt=media&amp;token=6fb7de49-fb0f-4fbf-951e-090a4a753954" alt=""><figcaption></figcaption></figure>

* jco

<figure><img src="https://3375851868-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhFAmY4z7d1R15Cv49vXQ%2Fuploads%2FiYtJX0QmnLgE05xbAj1G%2FScreenshot%202024-01-10%20at%2015.30.36.png?alt=media&amp;token=7d602103-34e3-498b-b486-a6b350380772" alt=""><figcaption></figcaption></figure>

* ucscgb

<figure><img src="https://3375851868-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhFAmY4z7d1R15Cv49vXQ%2Fuploads%2F3LmKGgaMjMgOFmWCJPRz%2FScreenshot%202024-01-10%20at%2015.31.27.png?alt=media&amp;token=bae369a0-1925-4988-9c03-e39208374450" alt=""><figcaption></figcaption></figure>