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
     b. Method: follow Rbase hclust description: hclust: Hierarchical Clustering

  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

## 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:

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