Question: How Do I Make A Heatmap In R?
0
gravatar for balagenotech
6.1 years ago by
balagenotech0 wrote:

Hi any one help me to draw heat map, i am having the three samples microbial diversity data, i wish to draw heat map in R statistics anyone replay how to upload data into R and draw heat map

R heatmap • 9.2k views
ADD COMMENTlink modified 5 weeks ago by srgk26ster10 • written 6.1 years ago by balagenotech0
5

This seems like a basic R usage question rather than a specific bioinformatics problem, so the answer would be "you need to learn how to use R."

ADD REPLYlink written 6.1 years ago by Neilfws48k
3

try to add actual data and desired output in your questions to make it answerable for us.

ADD REPLYlink written 6.1 years ago by Nari870

I put some code here before A: Superimpose 2 heatmaps

ADD REPLYlink written 6.1 years ago by Pavel Senin1.9k

Heatmap using R, with special conditions !!! might be quite close

ADD REPLYlink written 6.1 years ago by Michael Dondrup46k

This question has been asked before on biostars: How to draw a Heat map for gene expression data?

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by oxana.sachenkova0

+1 on Neilfws's response. There are MANY tutorials on how to draw a heatmap in R, just use google, they are out there. This is not a strictly bioinformatics question, rather a question about a common way to communicate data.

You didn't give us much information on what you are doing? You mention "three samples microbial diversity data" and I'm wondering if you mean to draw a correlation map (such as Pearson's, Spearman's etc. etc.) as they are a type of heat map and not a heat map of transcript data?

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by Josh Herr5.6k

Hello,

For R clustering there is an easy way in Galaxy. Go to the toolshed https://toolshed.g2.bx.psu.edu/ and look for tool named heat_map_creation. It is explained how to run on YouTube It allows one to enter a input matrix and uses R clustering techniques (you select from menu) and creates a heatmap to visualize in Galaxy as well.

Another way is via a self-contained Docker container Sincerely, Dr. Bob

ADD REPLYlink written 2.2 years ago by rbrownf0
7
gravatar for Nicolas Rosewick
6.1 years ago by
Belgium, Brussels
Nicolas Rosewick7.7k wrote:

check here :

http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/heatmap/

ADD COMMENTlink written 6.1 years ago by Nicolas Rosewick7.7k

Nice tutorial. But it does not handle multiple side color bars. The last plot in the tutorial is heatmap.2. This function is improved by heatmap.3 How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by Irsan6.9k
5
gravatar for Bioch'Ti
6.1 years ago by
Bioch'Ti1000
France (Avignon)
Bioch'Ti1000 wrote:

ggplot2 and heatmap plus are two easy to handle R packages! Check them out:

  1. http://www.r-bloggers.com/using-r-correlation-heatmap-with-ggplot2/

  2. http://cran.r-project.org/web/packages/heatmap.plus/heatmap.plus.pdf

ADD COMMENTlink modified 6.1 years ago by Eric Normandeau10k • written 6.1 years ago by Bioch'Ti1000
0
gravatar for Irsan
6.1 years ago by
Irsan6.9k
Amsterdam
Irsan6.9k wrote:

Most likely you want to make a heatmap with the following options:

  • Plot a dendrogram of clustering on both colums and rows of the heatmap
  • Plot multiple sample information colors on rows or columns
  • A legend that tells you how the intensity of the colors corresponds with the values that went into the heatmap

If you want all three of them, then you can either use ggplot2 but you will have difficulties with aligning the dendrogram plots with the heatmap. You will have to do something nasty like playing the viewport settings. Or you can go with the How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?

ADD COMMENTlink written 6.1 years ago by Irsan6.9k
0
gravatar for srgk26ster
5 weeks ago by
srgk26ster10
srgk26ster10 wrote:

HI! I appreciate that this has been a long time since your question, but you or anyone else reading this may be interested in this. I just developed a Julia-based GUI tool to plot heatmaps based on Python's Seaborn package, just for the reason you wanted. Though it doesn't make use of R. Just 10-15 min to get it running. Very minimal/no coding is required for this. Just need to click to input .xlsx/.csv/.txt files and a heatmap would be produced. At the minute, only heatmaps are supported. In the near future, additional plotting types and functionalities will be supported. This is the link with the full information and instruction:

https://github.com/srgk26/easy_plotting.app

ADD COMMENTlink written 5 weeks ago by srgk26ster10
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