Triangle heatmap with heatmap.2
Hi! How can I have a triangle heatmap (upper or lower) with heatmap.2 without disturbing the clustering?
heatmap.2
triangle
clustering
• 3,200 views
•
link
written
by
Poorya Parvizi
6
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
wombat covariance estimation
written by Bushra Bibi 8I need to run wombat tool but i am stuck in creating parameter file. Please guide how can i calculate upper triangle of random effects …
-
Kruskal-Wallis on more than one independent variables in R
written by Poorya Parvizi 6I have data which contains two independent variables and it does not follow the normal distribution. I checked it with the Shapiro test. However, I …
-
Batch effect correction in DE analysis of single cell RNA-seq data and visualization
written by Poorya Parvizi 6Hi Everyone, In my experiment, I have cells (same cell type) with 5 different drug treatments. These cells are sequenced in 3 batches and the …
-
Differential Expression Analysis with monocle and batch effect correction
written by Poorya Parvizi 6Hi, I would like to run differential expression analysis on my single-cell data. My data contains of 5 groups which sequenced in 3 batches. Each …
-
Cut one subcluster from heatmap and then paste it using R
written by lawarde.ankita1 7Hello Sir/madam, I have total 304 DEG and i have clustered them using hclust and heatmap.2 is used to plot the heatmap. ![heatmap][1] [1]: https://ibb.co/nfwZ3H …
-
Control samples size is much lower than tumor samples in TCGA
written by Poorya Parvizi 6I have tried to use TCGA glioblastoma RNA-seq samples to apply differential expression. However i realized that the number of "Solid tissue Normal" is much …
-
extracting the genes associated with the clusters
written by Bogdan 144Dear all, after clustering a gene expression dataset (with heatmap.2, or pheatmap), please can you advise, how can i extract the group of gene names …
-
Can I make a not clustered heatmap with MetaPhlAn
written by bidan67 0I want to make a heatmap with MetaPhlAn without clustered results. I have done the merging part. But as I looked through the manual of …
-
Does anybody know how to add a color side bar which will be re-ordered by the clustering in pheatmap
written by sw.arker 7Hello, I am recently starting to use pheatmap since it can draw more decent heatmap (personal opinion) in comparison with heatmap.2 or heatplot.. however, I …
-
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
written by Michi 99In the latest version of Gitools, [Gitools v2.1][1], we have improved the clustering of heatmaps. Here we explain in detail on how to perform and …
Something like a corrplot?
Yes. But corrplot's problem is, the data must range from -1 to 1. In addition, I need dendrogram in my heatmap.
Have you searched the WWW? By only having a triangular heatmap, you would be excluding many data-points from which the very cluster dendrograms that you want to include would have been produced. You may need to be more specific. Have you seen some plot in a publication?
I can think how I would go about doing this via the
pairs()functionality, but it's not a rudimentary task.