Question

how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)

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thindmarsmission ▴ 10

@thindmarsmission-17577

Last seen 6.2 years ago

Hi!!

I want to plot trends between genes across different conditions from my normalized count matrix (featurecount-EdgeR).

I was using "csCluster" in cummerbund. Now I switched to this pipeline and I am wondering, if similar pacakage or tool is available for plotting those kinds of trends. eg : below image (ref:cummerbund kellis lab)

https://www.google.de/search?q=cummerbund+cscluster&source=lnms&tbm=isch&sa=X&ved=0ahUKEwil_eWVheXdAhUixYUKHSfVBbQQ_AUIDigB&biw=1920&bih=1076#imgrc=5-d88IDIi9WRCM:

edger clustering visualization • 1.2k views

ADD COMMENT • link updated 6.2 years ago by James W. MacDonald 67k • written 6.2 years ago by thindmarsmission ▴ 10

score 2 · Accepted Answer · 2018-10-01

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 3 hours ago

United States

Those are just regular line plots from ggplot2. There is (literally) a metric ton of questions/answers about doing stuff with ggplot2, which you can easily Google for.

ADD COMMENT • link 6.2 years ago James W. MacDonald 67k

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Thank you, but for clustering the genes having similar trends throughout, what I can use ? I am new to this field. sorry for stupid questions.

ADD REPLY • link 6.2 years ago thindmarsmission ▴ 10

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The csCluster function uses pam (partitioning around medioids) from the cluster package.

ADD REPLY • link 6.2 years ago James W. MacDonald 67k