Interactive.Rmd

---
title: "Interactive examples"
author: "Leo Lahti, Sudarshan Shetty et al. `r Sys.Date()`"
bibliography: 
- bibliography.bib
output:
  BiocStyle::html_document:
    number_sections: no
    toc: yes
    toc_depth: 4
    toc_float: true
    self_contained: true
    thumbnails: true
    lightbox: true
    gallery: true
    use_bookdown: false
    highlight: haddock
---
<!--
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteIndexEntry{microbiome tutorial - Interactive}
  %\usepackage[utf8]{inputenc}
  %\VignetteEncoding{UTF-8}  
-->


## Interactive plots

```{r interactive-example, warning=FALSE, message=FALSE, fig.height=5, eval = TRUE}
library(ggplot2)
library(rvg)
library(ggiraph)
library(microbiome)
data("atlas1006")
pseq <- atlas1006
x <- microbiome::transform(atlas1006, "compositional")

mytheme_main <- theme( panel.background = element_blank(), 
  panel.grid.major = element_line(colour = "#dddddd"), 
  axis.ticks = element_line(colour = "#dddddd") )

mytheme_map <- theme(
  panel.background = element_blank(), axis.title.x = element_blank(),
  axis.text = element_blank(), axis.line.x = element_blank(),
  axis.line.y = element_blank(), axis.title.y = element_blank(),
  axis.ticks.x = element_blank(), axis.ticks.y = element_blank() )

df <- as(sample_data(x), "data.frame")
df$Dialister <- get_sample(x, "Dialister")
df$Prevotella <- get_sample(x, "Prevotella melaninogenica et rel.")
df$sample <- row.names(df)

# geom_point_interactive example
gg_point_1 <- ggplot(df, aes(x = Prevotella, y = Dialister, 
        color = age, tooltip = sample) ) + 
    geom_point_interactive(size=3)

# htmlwidget call
ggiraph(code = {print(gg_point_1 + mytheme_main)})
```