Creating a Heatmap in R | ComplexHeatMap tutorial p1

Google heatmap in Bioinformatics make me realize how much heatmap is being used in the world of bioinformatics research and publication. With the advancement in the codes, it is now possible for anyone with about an hours time to learn how to make a really intricate and beautiful figure without intensive knowledge in coding, or graphic design (like me, these thumbnail are created in LibreOffice draw).

While researching for how to use oncoprint, I came across this package call "ComplexHeatmap" in Bioconductor which was first publish in 2016 by Zuguang Gu and just find it impossible not to share about my journey in understanding the basics in using this package to draw out some pretty nice figures.

Find the script here

Find the website of the book here

Paper:
Gu, Z., Eils, R. and Schlesner, M., 2016. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics, 32(18), pp.2847-2849.

[PeihuiBrandonYeo]

0:00 Introduction to video content
1:08 Why the R markdown format
1:33 installing package and loading ComplexHeatmap into R
2:40 Making the data matrix
3:23 Heatmap() on all default settings
4:40 Changing the colors
6:50 Dealing with outliers in heatmap- data transformation
7:48 RAINBOW!!
8:40 Discrete matrix
10:26 Dealing with NA in data
11:20 Columns and row tittles

12:22 Clustering dendrogram
13:10 Size of dendrogram
14:40 clustering function
15:37 Using dendextend
17:25 Reordering rows, row and column tittles
20:57 row or columns split
24:30 Putting everything together

[AlexPreboy]

Please consider saying no to background music

[darshiv_]

hello, how can we sort the x axis values in alphabetical order ? my files are named form r1 to r9 and they are not in order.

[mebratuify]

How can we do heatmap spearman correlation graphs? Thank you so much.

[neurostudywithme]

thank you. but how can I sort my heat map based on my marker genes per cluster. In articles they show a very nice heat map figure where the expression of genes per cluster goes like a line..how can I do that

[hanifullah]

Actually i have gene expression data of about 19000 gene and 90 samples, so i want to know how can i narrow down my expression data ?

[smraza]

Hi can you make a video on diagonally split tiles heatmaps in seaborn and triangulation packages of python

[johnathonmcl]

Can the matrix be loaded in from an excel file? Will this hinder the rest of the code? Thanks for the great videos

[lvn]

Help all my damn colnames have pasted together and copied onto every column aidhdvdv they’re not individual!!!!