Comments on: Heatmap in R: Static and Interactive Visualization

By: Imran

Imran — Mon, 09 Oct 2023 02:47:29 +0000

What does (256) mean in the color code?

By: Eldunari

Eldunari — Fri, 23 Sep 2022 11:57:12 +0000

Hi Kassambara,

Thanks for your tutorials, it’s really helpfull.

Concerning the “Application to gene expression matrix” part, i was wondering if you can choose spceific color for each type (for instance “protein coding” in red and “other” in black in your example) .
If so, let me know 🙂

Thank again,

Eldu

By: James M. Melott

James M. Melott — Fri, 18 Feb 2022 16:03:06 +0000

Have you ever tried using the NGCHMR package for making interactive heatmaps using R?
https://github.com/MD-Anderson-Bioinformatics/NGCHM-R

https://bioinformatics.mdanderson.org/public-software/ngchm/

By: Ezequiel

Ezequiel — Tue, 04 May 2021 01:39:34 +0000

Hey Kassambara, thanks for doing this posts and the site, I find myself using it rather often. I was wondering how is that scale() works with the mtcars as it looks like the whole data frame is not numeric (car numbers). Thanks a lot!

By: Fernanda Anselmo-Moreira

Fernanda Anselmo-Moreira — Tue, 30 Mar 2021 19:29:50 +0000

Hi Kassambara,

I tried to follow the steps given in the course to make a simple heatmap with my own data, but I received the following error message:

> bamboo head(bamboo, n = 8L)
Compounds LeavesDS LeavesRS CulmsDS CulmsRS
1 Arachidic acid 0.00 0.00 3.08 2.47
2 Behenic acid 0.00 0.00 3.43 2.52
3 Heptadecanoic acid 0.66 1.43 5.22 5.51
4 Hexacosanoic acid 3.61 3.58 9.57 9.81
5 Lignoceric acid 0.54 1.21 5.51 6.39
6 Linoleic acid 23.14 35.24 78.13 109.18
7 Linolenic acid 133.28 201.37 66.01 64.60
8 Myristic acid 0.00 1.70 4.32 2.37
> df bambooscale heatmap(bambooscale, scale = “row”)

I would like to know what I need to do to consider my column with categorical data in the heatmap, like the example using mtcars data.

Thanks!!!

By: kassambara

kassambara — Fri, 10 Jul 2020 14:33:54 +0000

In reply to Qing. Thank you for your input, I will do that!

By: Qing

Qing — Fri, 10 Jul 2020 12:29:21 +0000

could you please write a tutorial of consensus clustering heatmap? thanks

By: Machetero

Machetero — Thu, 30 Apr 2020 16:59:51 +0000

Hi Kassambara,

is there any chance to do the same heatmap without the mtcars legend? This may lead to a single colour in the heatmap. A single color in the heatmap with my own categorical variables is what I trying to do.

Also, when scaling the data, I tried to scale using the euclidean distance.. but then I can not make the heatmap. which distance is used by default when df <- scale (df)?

Thank you

By: kassambara

kassambara — Sat, 25 Apr 2020 22:21:25 +0000

In reply to Machetero.

Thank you for pointing this out.

The error was due to an update to the ComplexHeatmap package.

I updated the article accordingly:

ha <- HeatmapAnnotation(
  cyl = mtcars$cyl, am = mtcars$am, mpg = mtcars$mpg,
  col = col
)

By: Machetero

Machetero — Sat, 25 Apr 2020 17:47:10 +0000

I had followed all the code but this error keeps popping up.

ha <- HeatmapAnnotation(annot_df, col = col)
Error: annotations should have names.

Any thought?