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JinmiaoChenLab / cytofkit

cytofkit: an integrated flow/mass cytometry data analysis pipeline
http://jinmiaochenlab.github.io/cytofkit/
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Heat Map from viSNE #74

Open kalsriv opened 4 years ago

kalsriv commented 4 years ago

Hi

Forgive my ignorance. I have been using cytofkit for viSNE analysis. I am looking at heatmap for an analysis of expression level. What is the best way to get the expression level of each of the markers from individual clusters? Do you want the users to look into each of the csv file from clusters and make an interpretation? Thanks in advance

Kalyan

SamGG commented 4 years ago

Hi. The first computation ends up with CSV files and PDF files. PDF files contain a heatmap (either mean or median) with all clusters at once. So it's easy to label/interpret each cluster relatively to the others or to the most/less intense values in each channel. I think you could also redo a heatmap using the interactive analysis tool of Cytofkit. This is very interesting for merging clusters and labelling them. See the cytofkitShinyAPP() function at https://github.com/JinmiaoChenLab/cytofkit#usage Best. PS: close this issue if your question is solved.