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Old 03-11-2012, 07:52 AM   #1
inankai
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Default How to plot peak density heat map

I just start to take the bioinformatics part of my ChIP-seq experiments. and it is not too difficult for me to do mapping and peak calling. but I want to make further analysis of my data.
Like, whether the transcription factor binding is significantly enriched in the promoters of genes belonging to the same pathway, TGFb for example. while not other pathways (JAK/STAT, Ras etc).

So, I want to plot the binding peaks at the promoter of a specific set of genes, and rank the peaks based on the distance to TSS.

Can anyone help to figure out, what software should I use?
Or I have to write the script by myself, if so, should I use perl?
I only have a bit of experience with Python.

I attached a similar example.
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File Type: jpg Peaks.JPG (86.2 KB, 290 views)
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Old 03-11-2012, 07:55 AM   #2
inankai
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Here is another example for this kind of heat map or high density peak map.
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File Type: jpg nature10006-f1.2.jpg (42.1 KB, 211 views)
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Old 03-18-2012, 06:16 AM   #3
inankai
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Please help about this topic.
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Old 03-26-2012, 12:00 PM   #4
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looks like a custom script is needed
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Old 03-26-2012, 12:11 PM   #5
honey
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Default plot

Seqminer will be closet to do this
http://bips.u-strasbg.fr/seqminer/tiki-index.php
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Old 03-27-2012, 11:25 AM   #6
inankai
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Thank you guys.
seqMiner seems do the job.
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Old 07-11-2012, 08:48 PM   #7
mathew
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Cool any one has script or software to plot such heat maps

I want revive this thread and would like to know if soemone can share the script here on forum or privatly or has any idea about a tool which can generate such heat maps of TSS distance vs tag density. Seqminer will not give thsi kind of Figure and is good mainly for Bam/ sam bed files of unprorocessed data.
i am sure there are number of users who will be intrested in such heat maps.
Thanks

Last edited by mathew; 07-12-2012 at 08:45 AM.
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Old 10-02-2012, 11:53 AM   #8
SF_mallish
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Hi Mathew,

Probably you can use the program from HOMER software.
http://biowhat.ucsd.edu/homer/ngs/quantification.html


Quote:
Originally Posted by mathew View Post
I want revive this thread and would like to know if soemone can share the script here on forum or privatly or has any idea about a tool which can generate such heat maps of TSS distance vs tag density. Seqminer will not give thsi kind of Figure and is good mainly for Bam/ sam bed files of unprorocessed data.
i am sure there are number of users who will be intrested in such heat maps.
Thanks
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Old 02-24-2013, 02:36 PM   #9
crazyhottommy
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Any python scripts for this kind of heatmap?
Thanks!
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Old 02-24-2013, 11:25 PM   #10
simonandrews
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You can make these kinds of plot in SeqMonk (called the aligned probes plot). You can put them over any arbitrary region of either fixed or variable sizes.
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Old 02-25-2013, 04:06 PM   #11
crazyhottommy
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Thanks so much! SeqMonk looks very powerful.
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Old 02-26-2013, 04:48 AM   #12
Luyi Tian
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you can plot heat map easily if you are familiar with matplotlib.

custom code would like this:
###########
from matplotlib import pyplot as PLT
from matplotlib import cm as CM
from matplotlib import axes

##create a figure and add a plot
fig = PLT.figure(facecolor='w')
ax1 = fig.add_subplot(2,1,1,position=[0.1,0.15,0.9,0.8])

##create a cmap object. it controls the color and some style in the heatmap
## you can change 'spectral' to other words. see the doc
cmap = CM.get_cmap('spectral', 1000)

##create heatmap use the DATA and the cmap. vmin and vmax are the minimum and maximum value in your data
map = ax1.imshow(DATA, interpolation="nearest", cmap=cmap,aspect='auto', vmin=0,vmax=15)

##then create the scale bar
cb = PLT.colorbar(mappable=map, cax=None, ax=None,shrink=0.5)
cb.set_label('Enrichment level')

##plot it
PLT.show()
###########
the DATA is like:
DATA=[
[1.4,2.2,4.7,6.1],
[4.1,13.5,15.0,1.9],
.....
]

this is the website: http://matplotlib.org/
it is very powerful. You can plot almost everything you want using this module

Last edited by Luyi Tian; 02-26-2013 at 04:50 AM.
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