From eab3b60f035d0256b0dcd70ceed22e62cb5e0cf3 Mon Sep 17 00:00:00 2001 From: brianpenghe Date: Fri, 5 Oct 2018 16:11:33 -0700 Subject: [PATCH] updated README clustering --- README.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 2f207c8..92a7400 100644 --- a/README.md +++ b/README.md @@ -52,15 +52,19 @@ Dispersion=var(PMBC_perc_filtered,0,2)./mean(PMBC_perc_filtered,2); [P I]=sort(Dispersion,'descend'); ``` -### Clustering and visualization +### Supervised Clustering and visualization -PMBCClg=clustergram(PMBC_perc_filtered(I(1:500),:),'Standardize',0,'DisplayRange',2.5,'Colormap',colormap(jet),'RowPDist','correlation','ColumnPDist','spearman','Symmetric',true,'linkage','complete', 'OptimalLeafOrder',false) +PMBCClg=clustergram(PMBC_perc_filtered(I(1:2000),:),'Standardize',0,'DisplayRange',7.5,'Colormap',colormap(jet),'RowPDist','correlation','ColumnPDist','spearman','Symmetric',false,'linkage','complete', 'OptimalLeafOrder',false) -screen shot 2018-09-03 at 2 17 16 pm +screen shot 2018-10-05 at 3 15 41 pm Now you get a clustergram which can be annotated interactively following [Matlab Clustergram Manual](https://www.mathworks.com/help/bioinfo/ref/clustergram.html) to make it look like the following -screen shot 2018-09-03 at 2 47 38 pm +screen shot 2018-10-05 at 4 10 16 pm + +And save (by right clicking) individual clusters into workspace as Cluster1, Cluster2 etc. + +screen shot 2018-10-05 at 3 33 42 pm #### Check expression of specific gene lists