venn.rmd

---
title: "Venn"
author: "Chuyao Wang"
date: "`r Sys.Date()`"
output: 
  html_document: 
    number_sections: true # automatic section numbering
    toc: yes # table of content
    toc_depth: 3
    toc_float: true
    smooth_scroll: true
    toc_collapsed: true
    fig_caption: yes
    df_print: kable
params:
    datadir: "./data/cellsample20220827"
knit: (function(inputFile, encoding) {
  rmarkdown::render(inputFile, encoding = encoding, output_dir = "./html") })
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(dplyr)
library(ggplot2)
library(openxlsx)
library(VennDiagram)
library(stringr)
library(RColorBrewer)
```

## Import datasets

> Need to use excel to add a blank worksheet to the xlsx file, or the function will not read!

```{r}
fls <- dir(params$datadir)
fls <- paste(params$datadir,fls,sep="/") %>% as.data.frame

samples <- apply(fls, MARGIN = 1, FUN = function (x) {
  a <- read.xlsx(x,sheet=1,na.strings="")
  return(a)
})
```

## De-duplicate

```{r}
compoundNames <- lapply(samples, function(x){
  names <- x$Name %>%
    unique
  return(names)
})
```

## Venn Diagram

```{r}
myCol <- brewer.pal(dim(fls)[1], "Pastel2") # Color for plotting
names.short <- str_split_fixed(unlist(fls),"/",n=4)[,4] # Extract file names

futile.logger::flog.threshold(futile.logger::ERROR, name = "VennDiagramLogger")
plt <- venn.diagram(
        x = compoundNames,
        category.names = names.short,
        filename = NULL,
        output=TRUE,
        
        # Image size
        height = 405,
        width = 720,
        resolution = 600,
        
        # Circles
        lwd = .5,
        fill = myCol,

        # Numbers
        cex = .6,
        fontface = "bold",
        fontfamily = "sans",

        # Set names
        cat.cex = 0.6,
        cat.fontface = "bold",
        cat.default.pos = "outer",
        cat.fontfamily = "sans")

grid::grid.draw(plt)


```