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
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
@@paolamontenegro517 Hi! Yea so what I'm doing is first I Find marker genes and make list for each cluster and using this list as features when I'm generating heat map. Also you can sort your clusters based on similarty
There are many ways to do that as it depends on the purpose of your research. The easiest way is to remove the low expression genes, or run a PCA or other dimensional reduction analysis and check the loading of the genes, which then, you can remove the genes with the least loading since it doesn't contribute to the separation of the different sample.
@@LiquidBrain Can you do a tutorial on doing a PCA on a big gene expression data set? I really want to know how to do the PCA analysis and how to actually reduce the dimension of my data set with PCA with code examples! Would be doing me a big favor!
@@LiquidBrain thank you for your reply! I am going to test the code out today, just one more question, could you possibly show how to clacupate the confidence interval to plot alongside the heatmap? Or are there any good resources that might help me with that?
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
Hi at 22.09 min for the kmean clustering does the dendrogram based on
Hierarchical clustering or kmean ?
Please consider saying no to background music
Excellent tutorial 😊
Nice tutorial!
Waiting for pt2
How can we do heatmap spearman correlation graphs? Thank you so much.
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.
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
Hi, I have the same question, Do you maybe get any answer?
@@paolamontenegro517 Hi! Yea so what I'm doing is first I Find marker genes and make list for each cluster and using this list as features when I'm generating heat map. Also you can sort your clusters based on similarty
awsome tutorial!! waiting for pt2
Oh, you can find all 4videos on the channel already
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 ?
There are many ways to do that as it depends on the purpose of your research. The easiest way is to remove the low expression genes, or run a PCA or other dimensional reduction analysis and check the loading of the genes, which then, you can remove the genes with the least loading since it doesn't contribute to the separation of the different sample.
@@LiquidBrain Can you do a tutorial on doing a PCA on a big gene expression data set? I really want to know how to do the PCA analysis and how to actually reduce the dimension of my data set with PCA with code examples! Would be doing me a big favor!
@@killa14108 I just uploaded a video on limma voom pipeline, that should be able to help you on this analysis
Help all my damn colnames have pasted together and copied onto every column aidhdvdv they’re not individual!!!!
Can the matrix be loaded in from an excel file? Will this hinder the rest of the code? Thanks for the great videos
As long as the data structure looks the same after you input, it should not actually matter :)
@@LiquidBrain thank you for your reply! I am going to test the code out today, just one more question, could you possibly show how to clacupate the confidence interval to plot alongside the heatmap? Or are there any good resources that might help me with that?
Calculate*
Hi can you make a video on diagonally split tiles heatmaps in seaborn and triangulation packages of python