---
title: "Interactive Volcano Plot"
format: 
    html:
        theme: none
        embed-resources: true
        fontsize: 1.1em
        linestretch: 1.7
author: "Guangchuang Yu\\

        School of Basic Medical Sciences, Southern Medical University"
date: "`r Sys.Date()`"
vignette: >
  %\VignetteIndexEntry{ivolcano introduction}
  %\VignetteEngine{quarto::html}
  %\VignetteEncoding{UTF-8}
---

```{r results='hide', echo=FALSE, message=FALSE}
library(yulab.utils)
```


## Prepare example data

```{r eval = FALSE}
library(airway)
library(DESeq2)
library(org.Hs.eg.db)
library(AnnotationDbi)

data("airway")

counts_mat <- assay(airway)
airway <- airway[rowSums(counts_mat) > 1, ]

dds <- DESeqDataSet(airway, design = ~ cell + dex)
dds <- DESeq(dds)
res <- results(dds, contrast = c("dex", "trt", "untrt"))

df <- as.data.frame(res)
df$gene_id <- rownames(df)
df$symbol <- mapIds(org.Hs.eg.db, 
                    keys = df$gene_id,
                    column = "SYMBOL", 
                    keytype = "ENSEMBL", 
                    multiVals = "first")

df <- df[!is.na(df$symbol), ]
df <- df[, c("log2FoldChange", "padj", "symbol")]

head(df)
```

```{r echo=FALSE}
f <- system.file('extdata/airway.rds', package='ivolcano')
df <- readRDS(f)
head(df)
```

## Interactive volcano plot



```{r ivocano, fig.width=10, fig.height=6}
library(ivolcano)

ivolcano(df,
        logFC_col = "log2FoldChange",
        pval_col = "padj",
        gene_col = "symbol",
        top_n = 5,
        onclick_fun=onclick_genecards)
```


We can use the `r CRANpkg("fanyi")` package to query NCBI gene description and translated to local language to be displayed on the plot, see also <https://yulab-smu.top/ivolcano/>.