README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  fig.width = 6,
  out.width = "100%",
  fig.retina = 3
)
```

# ggsegJHU <img src='man/figures/logo.png' align="right" height="138.5" />

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Contains data for ggseg and ggseg3d for the JHU white matter segmentation.

Hua et al. (2008) NeuroImage, 39(1):336-347 [pubmed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2724595/)

## Installation
We recommend installing the ggseg-atlases through the ggseg [r-universe](https://ggseg.r-universe.dev/ui#builds):

```{r eval = FALSE}
# Enable this universe
options(repos = c(
    ggseg = 'https://ggseg.r-universe.dev',
    CRAN = 'https://cloud.r-project.org'))

# Install some packages
install.packages('ggsegJHU')
```

You can install the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("LCBC-UiO/ggsegJHU")
```
## Example

This is a basic example which shows you how to solve a common problem:
```{r}
library(ggsegJHU)
```

```{r, fig.height=6}
library(ggseg)
library(ggplot2)

plot(jhu) +
  theme(legend.position = "bottom",
        legend.text = element_text(size = 7)) +
  guides(fill = guide_legend(ncol = 2))

```

```{r "noneval", eval=FALSE}
library(ggseg3d)
library(dplyr)

ggseg3d(atlas = jhu_3d) %>% 
  add_glassbrain("left") %>% 
  pan_camera("right lateral")
```

```{r "orca", include=FALSE}
library(ggseg3d)
library(dplyr)

p <- ggseg3d(atlas = jhu_3d) %>%
  add_glassbrain("left") %>% 
  pan_camera("right lateral") %>%
  plotly::add_annotations( text="Screen capture",
                  legendtitle=TRUE, showarrow=FALSE,
                  font = list(color = "#000000b4",
                              family = 'sans serif',
                              size = 50))
plotly::orca(p, "man/figures/README-3d-plot.png")
```

```{r "incl", echo=FALSE}
knitr::include_graphics("man/figures/README-3d-plot.png")
```

Please note that the 'ggsegJHU' project is released with a
[Contributor Code of Conduct](CODE_OF_CONDUCT.md).
By contributing to this project, you agree to abide by its terms.