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A brief tutorial about how to use Heatmap Maker, a web application in R made with Shiny.
What is Heatmap Maker?
Heatmap Maker is a Shiny App that allows you to make and save cluster heatmaps as the following:
Heatmap Maker has as a core the function heatmap.2() from gplots package.
Install and use
If you are an R and RStudio user, you have two options to use the app.
Download from GitHub
Simply download it from GitHub or through GitHub Desktop, just click here Heatmap Maker. Once in the HeatmapMaker main folder, double click on the Heatmap-Maker.Rproj file:
And type in the R console (you need devtools package):
devtools::laod_all(".")
then:
HeatmapMaker()
As a package
Install the app as a package with the next code:
devtools::install_github("jpch26/Heatmap-Maker")
then:
library(HeatmapMaker)
and finally:
HeatmapMaker()
Shinyapps.io
Use the app directly, you do not need R or RStudio, by clicking in the next link:
Probably, this will not be a long term option to use the app because shinyapp.io just allow to publish five apps simultaneously, which also includes some other restrictions. I hope in the future I will able to find a good solution for this (or maybe I will pay for it…).
Data sets
Heatmap Maker accepts TSV, TXT and CSV files. I recommend the next structure for your data (for more clarity presented in a Excel sheet):
At this example, columns (column names in orange) represent an independent variable and rows (row names in blue) represent a dependent variable or response. The above is not exhaustive and will rely on your data, maybe you will have two independent variables.
The only requirement is that your data set follows the “matrix” structure showed in the figure. You can see more examples of data sets in the github repository for this app.
Available colors
The available colors are:
All the used colors in the app are colorblind friendly.
Steps
The first time you open the app, it will display a pre load data set. You can find this data set in the repository for this app, search for it in the sample_data folder as expression_data_1, available in .txt, .tsv, and .csv formats.
The app and the pre load heatmap will look like this:
Upload your data
Just click on upload data and search for your data set:
The plot will be updated automatically to represent your data.
Customize
Customize your heatmap with the different options in the option side bar.
- X label: Write a label in the x axis.
- Y label: Write a label in the y axis.
- Heatmap color: Choose a color palette for the values in your heatmap.
- Dendrogram: Display, or not, dendrograms in rows and/or columns.
- Side colors: Put or remove side colors on columns and/or rows.
- Heatmap row names and Heatmap column names: Put or remove row and column names, respectively. This names will be take directly from your data set.
- Adjust x label and Adjust y label: Adjust the position of x and y labels, respectively.
- Adjust column name size and Adjust row name size: Adjust sizes for row and column names.
Download
Be sure to write a good name for your plot, choose a format, and finally click on Download Heatmap.
Your image will be located in your downloads directory.
GitHub Repository
If you want to check out the repository for this app just click on:
This repository includes data sets that you can use to explore the app features, check out the sample_data directory.
Thank you so much for your time and visit this site.
Juan Pablo Carreón Hidalgo 🤓
jpch_26@outlook.com
https://twitter.com/JuanPa2601
The text on this tutorial is under Creative Commons Attribution 4.0 International License.
Heatmap Maker is under GNU General Public License v3.0
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