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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/"
)
```
# GiottoVisuals <img src="man/figures/logo.png" align="right" alt="" width="160" />
<!-- badges: start -->
![Version](https://img.shields.io/github/r-package/v/drieslab/GiottoVisuals)
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![codecov](https://codecov.io/github/drieslab/GiottoVisuals/graph/badge.svg?token=F4ga1Ahbhw)](https://codecov.io/github/drieslab/GiottoVisuals)
[![R-CMD-check](https://github.com/drieslab/GiottoVisuals/actions/workflows/main_check.yml/badge.svg)](https://github.com/drieslab/GiottoVisuals/actions/workflows/main_check.yml)
[![GitHub issues](https://img.shields.io/github/issues/drieslab/Giotto)](https://github.com/drieslab/Giotto/issues)
[![GitHub pulls](https://img.shields.io/github/issues-pr/drieslab/GiottoVisuals)](https://github.com/drieslab/GiottoVisuals/pulls)
<!-- badges: end -->
GiottoVisuals contains the main plotting functions of Giotto Suite
## Installation
You can install GiottoVisuals like:
``` r
if (!requireNamespace("pak", quietly = TRUE)) install.packages("pak")
pak::pak("drieslab/GiottoVisuals")
```
## Script Organization by Prefixes:
`aux_` - auxilliary and meta functionality
- `aux_output.R` - plot output handling
- `aux_save.R` - plot saving
- `aux_defaults.R` - set plotting defaults
- `aux_visuals.R` - general auxilliary plotting functions
`plot_` - general plotting functions organized by type of plot
- `plot_scatter.R` - scatter plots
- `plot_violin.R` - violin plots
- `plot_heatmap.R` - heatmaps
- `plot_dendrogram.R` - dendrograms
`vis_` - specific plotting functions organized by topic
- `vis_spatial.R` - plotting with aggregated information
- `vis_spatial_in_situ.R` - plotting with raw points and polygons information
`gg_` - ggplot2 related
- `gg_info_layers.R` - modular internals for plotting the different layers of information
- `gg_annotation_raster.R` - image pipeline
Other:
- `color_palettes.R` - color palettes and factory functions
- `vis_spatialDE.R` -
Package:
- `package_imports.R` - all imports
- `globals.R` - global variables
- `dd.R` - dummy documentation for inheriting
- `zzz.R` - onloads