Hi all,
I have the following RNA-Seq dataset:
An example row of the dataset:
ID Gene.ID Gene.symbol logFC AveExpr t P.Value adj.P.Val
223597_at 55600 ITLN1 -9.669889 0.8438350 -50.27410 3.61e-60 1.98e-55
I would like to create a heatmap of these genes in the whole dataframe and also then create a heatmap with just selected number of genes in the dataframe in R.
Can you please help me with this?
Many Thanks,
Ishack
ComplexHeatmap is a great R package to create heatmaps.
ComplexHeatmap examples
You probably want to use a table of expression values, not stats.
Hints to help you get started: You need a bunch of
geom_rect
s withfill=logFC
and a manual gradient color scale withhigh=red, low=blue, middle=white
Hi All, Thanks very much for your help,
I found a way finally to create a heatmap for the RNA-seq data.
But I how can I group the different samples into the 2 different groups and compare them, please?
GSM997591 GSM997592 = Control
GSM997593 GSM997594 GSM997595 = Disease
I have chosen to use the raw expression values as recommended.
x-axis = experimental groups
y axis = axis gene name
Any help would be greatly appreciated.
Ishack
you may get some help from this post
Hi Prakash,
That post is a bit useful but very hard to understand, can you please give me some code examples?
Many Thanks,
Ishack
When you group observations, you're going to need to aggregate the values somehow. Pick an aggregation logic (mean/median/something that makes sense) and plot that. I do sense you're already losing sight of what's important when you plot a heatmap. When you group and plot an aggregate, your plot will in no way help derive insights into your data. It can only be used to visualize obvious disparities between the groups.
Thanks RamRS for the insight.
Stop adding new posts as answers unless you’re actually posting a solution to the question.
https://ibb.co/Wz6wfyX
Hi Guys, this is the heatmap I have created. Can you tell me please if this is biologically meaningful?
Many Thanks,
Ishack
Is this an assignment of some sort? Why are you seeking help with both creating the heatmap and interpreting it? Also, please see How to add images to a Biostars post to add the image properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)
Apologies, this is not an assignment. I just need help creating the heatmap. I just wanted your opinion on how it looks visually.
We know essentially nothing about your experiment, how could we tell you what’s biologically meaningful?
Here I can see some faint signal but clustering of columns and rows needed to really see if you have a proper separation of your data across meaningful biological condition of interest. Again if you are new, scan the blogs well to see a tutorial, there are plenty floating in biostars and some amazing blog posts of real data using various R packages for heatmap visualization with code snippets.