# CHeatmapShiny

**Repository Path**: shawnmagic/CHeatmapShiny

## Basic Information

- **Project Name**: CHeatmapShiny
- **Description**: A shiny app for simple heatmap based on  ComplexHeatmap
- **Primary Language**: R
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-08-25
- **Last Updated**: 2022-07-01

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# CHeatmapShiny App
**Required R 4.1, please update R to version 4.1**

Based on ComplexHeatmap. A simple shiny app for upload files to generate heatmap by CoomplexHeatmap.

## Content
- Data cleaning
	1. **Missing value treatment**  

		a. remove entire row: `dplyr::drop_na` 
 
		b. replace NA value with a customized value.  

	2. **Noise remove**  

		a. `sample_percetage`: eg: remove genes which has fpkm value less than `noise_cutoff` of `sample_percetage` samples. 
 
		b. `noise_cutoff`:   
   
		c. If do not need, choose "none"  

- Data normlization 
	1. **log transfer**  

		a. log2(x) or  log10(x)   

		b. log2(x+1) or log10(x+1)  

	2. **Z-score**

		a.  row-scale  

		b.  column-scale  


- Cluster
	1. **Hclust**  
 
		a. Distance: follow Rbase dist description: [dist: Distance Matrix Computation](https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/dist)  
		b. Method: follow Rbase hclust description: [hclust: Hierarchical Clustering](https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust)  

	2. **Kmeans**

		a. kmeans center number. how many groups you want.  

 		b. kmeans repeat time. Since the selection of the center point of k-means is random each time, it is recommended to increase the number of repetitions to ensure the stability of the result.  


- Annotation
	1. **Location**  

		a. For column annotation top or bottom  

		b. For row annotation left or right  

		c. bugs: legend will mix all groupname because I haven't thought of a better way to separate them now.  


## Install

```R
## install dependence
if (!require('devtools')) install.packages("devtools");
if (!require('tidyverse')) install.packages("tidyverse");
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager");
if(!require('ComplexHeatmap')) devtools::install_github("jokergoo/ComplexHeatmap");
if(!require('InteractiveComplexHeatmap')) devtools::install_github("jokergoo/InteractiveComplexHeatmap");
## install CHeatmapShiny
if (!require('CHeatmapShiny')) devtools::install_github("ShawnWx2019/CHeatmapShiny");
```

## Usage:

```R
library(CHeatmapShiny)
library(tidyverse)
options(shiny.maxRequestSize = 300*1024^2) ##if your upload matrix is soooo big, please run the code first!
run_CheatmapShiny()
```