Question

How can I show certain gene's expression in clusters by sc3

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qq1493438060 • 0

@qq1493438060-15919

Last seen 6.2 years ago

I'm a college student and use sc3 for my graduation thesis. I have got 3 clusters and the expression matrix. I want so show certain gene`s expression in heatmap besides marker genes and DE genes. How can I do it？Thanks！

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ADD COMMENT • link updated 6.5 years ago by Vladimir Kiselev ▴ 150 • written 6.5 years ago by qq1493438060 • 0

score 0 · Answer 1 · 2018-05-25

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Vladimir Kiselev ▴ 150

@vladimir-kiselev-9342

Last seen 5.6 years ago

Sanger Institute, Cambridge, UK

I don't think this is related to SC3. You can use the pheatmap package to visualise any genes you like. The heatmap will look similar to SC3, since it's also using pheatmap.

ADD COMMENT • link 6.5 years ago Vladimir Kiselev ▴ 150

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Thank you for your answer！This is the first time for me to use R for bioinformatics. I will learn how to use pheatmap package.

I just want to show certain genes' expression in clusters provided by sc3 besides mark genes and DE genes. How can I find these rows of SingleCellExperiment and show them on heatmap by pheatmap or any other way？（The rowname is gene'name）

ADD REPLY • link 6.5 years ago qq1493438060 • 0