6 votes

Is it possible to get such a plot

While it was easy to get your data after your edit, the data was not quite useful, the second data frame/matrix has 2 columns only! I had to create a fake data set, that looks like this: ...
haci's user avatar
  • 4,112
4 votes
Accepted

plotMA function issue: can not circle genes

It's likely that the fold-change of the topGene is greater than 5. Consequently, the circle is being drawn and the text produced, but they're outside the bounds of ...
Devon Ryan's user avatar
  • 19.6k
3 votes
Accepted

How I can reproduce this heat map

In case it is still helpful as the post is rather old, the code below would generate a heatmap with annotations thanks to the ComplexHeatmap package. But before ...
haci's user avatar
  • 4,112
1 vote

How to transform and sort the matrix to make a heatmap showing signatures?

You are almost there except for a few tricks: If you want columns to be ordered using the values in Cell 4, you will need to provide a custom column order either with the ...
haci's user avatar
  • 4,112
1 vote
Accepted

log2fold change as heatmap

If I read quickly thru the paper, I see you refer to Fig 5D. In the methods they describe that they use Fluidigm (i.e. RT-qPCR) for gene expression, not RNA-seq. The data link you give is for small-...
benn's user avatar
  • 3,571

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