SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
cummeRbund get isoforms paolo.kunder Bioinformatics 6 04-23-2014 07:59 AM
Biological replicates with cuffdiff, cummeRbund turnersd Bioinformatics 15 11-19-2012 05:59 AM
Coverage plots for paired end data swebb Bioinformatics 0 12-12-2011 01:59 AM
tag density plots bogdan RNA Sequencing 0 12-03-2010 10:44 PM
overlaying coverage plots zlu Bioinformatics 5 08-23-2010 01:49 AM

Reply
 
Thread Tools
Old 12-13-2011, 01:55 PM   #1
Carlos Borroto
Member
 
Location: Baltimore, MD

Join Date: Mar 2011
Posts: 19
Default What is the meaning density in CummeRbund plots?

Hi,

I recently started using CummeRbund for downstream analysis of cuffdiff output. Really nice tool BTW. I can't figured out exactly how to read the density plot:
http://compbio.mit.edu/cummeRbund/manual.html#Global

Any help on this? What is the meaning of density in this context?
Thanks,
Carlos
Carlos Borroto is offline   Reply With Quote
Old 12-16-2011, 12:52 PM   #2
lgoff
Member
 
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82
Default Density plot

Hi Carlos,
You can think of the density as a 'smoothed' representation of a histogram. In this particular case, the csDensity plot is being used to examine the distribution of FPKM values across individual samples.

Check out http://en.wikipedia.org/wiki/Kernel_density_estimation for more specific information on what is being represented.

Thanks for trying cummeRbund!

Cheers,
Loyal
lgoff is offline   Reply With Quote
Old 12-18-2011, 10:41 AM   #3
Carlos Borroto
Member
 
Location: Baltimore, MD

Join Date: Mar 2011
Posts: 19
Default

Thanks for the answer, I understand now.

Looking forward for the cookbook recipes.
Carlos Borroto is offline   Reply With Quote
Old 04-06-2012, 01:08 PM   #4
apadr007
Member
 
Location: washington DC

Join Date: Oct 2011
Posts: 21
Default

Since we're on the subject, what is the criteria for something having significance in volcano plots?

I noticed that in some of my graphs my p-value may be less than 0.05 and not be significant according to whats plotted. Can you please elaborate on this.

Much appreciated,
apadr007 is offline   Reply With Quote
Old 04-07-2012, 08:57 AM   #5
lgoff
Member
 
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82
Default

Quote:
Originally Posted by apadr007 View Post
Since we're on the subject, what is the criteria for something having significance in volcano plots?

I noticed that in some of my graphs my p-value may be less than 0.05 and not be significant according to whats plotted. Can you please elaborate on this.

Much appreciated,
Hi apadr007,
The significance calls in cummeRbund were originally done against the 'significant' output field from cuffdiff. This was across the board as we were letting cuffdiff decide on a significance threshold. We have since implemented the MTC in cummeRbund and you can specify your own alpha for calls to 'getSig()' for example. However, to your point, I have neglected to include this in the csVolcano plotting methods. So as of now, it's still plotting on the original 'significant' field from cuffdiff. I will make this change for a future version such that you can either turn off the significance callouts and/or provide an alpha value to csVolcano on which to draw your significance threshold.

Thanks for pointing this out!

Cheers,
Loyal
lgoff is offline   Reply With Quote
Old 04-09-2012, 03:00 AM   #6
billstevens
Senior Member
 
Location: Baltimore

Join Date: Mar 2012
Posts: 120
Default

Quote:
Originally Posted by lgoff View Post
Hi Carlos,
You can think of the density as a 'smoothed' representation of a histogram. In this particular case, the csDensity plot is being used to examine the distribution of FPKM values across individual samples.

Check out http://en.wikipedia.org/wiki/Kernel_density_estimation for more specific information on what is being represented.

Thanks for trying cummeRbund!

Cheers,
Loyal
Hi,
I also have a quick question on the graph. Since its a log graph, does this graph just not show FPKM values less than 1? One of the reasons I am wondering is because my probability density function (just for from eyeing it) looks like it is less than 1.
billstevens is offline   Reply With Quote
Old 04-09-2012, 12:57 PM   #7
apadr007
Member
 
Location: washington DC

Join Date: Oct 2011
Posts: 21
Default

Thank you, Loyal. Also, how can one generate a table based on the data that csVolcano is plotting? The reason I ask is because after manually inspecting my cuff diff output I am not seeing some of the extremely high points csVolcano is plotting. So is there a way to produce a txt file from csVolcano as well as its graph?
apadr007 is offline   Reply With Quote
Old 04-10-2012, 02:16 PM   #8
sdriscoll
I like code
 
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438
Default

Quote:
Originally Posted by billstevens View Post
Hi,
I also have a quick question on the graph. Since its a log graph, does this graph just not show FPKM values less than 1? One of the reasons I am wondering is because my probability density function (just for from eyeing it) looks like it is less than 1.
I think in the log plots where they are plotting FPKM values they add 1 to the data. If you don't the density plot looks totally different.

try this in R (assuming you imported your data to a variable 'cuff' and your samples are named 'sample1' and 'sample2').

plot(density(diffData(cuff@genes,"sample1","sample2")$value_1))

verses

plot(density(diffData(cuff@genes,"sample1","sample2")$value_1+1))

R's kernel density algorithm extends the smoothed line past the actual extent of the data its smoothing. So you'll see the density line go below 1 even if 1 is the lowest value.
sdriscoll is offline   Reply With Quote
Old 04-17-2012, 04:52 PM   #9
lgoff
Member
 
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82
Default

Quote:
Originally Posted by billstevens View Post
Hi,
I also have a quick question on the graph. Since its a log graph, does this graph just not show FPKM values less than 1? One of the reasons I am wondering is because my probability density function (just for from eyeing it) looks like it is less than 1.
Hi Bill,
For the csDensity plot, (and in general), when logMode=T then a pseudocount (accessible as 'pseudocount' argument and default=1) is added prior to log transformation.

Loyal
lgoff is offline   Reply With Quote
Old 04-17-2012, 04:53 PM   #10
lgoff
Member
 
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82
Default

Quote:
Originally Posted by apadr007 View Post
Thank you, Loyal. Also, how can one generate a table based on the data that csVolcano is plotting? The reason I ask is because after manually inspecting my cuff diff output I am not seeing some of the extremely high points csVolcano is plotting. So is there a way to produce a txt file from csVolcano as well as its graph?
The csVolcano is generated from data that can be retrieved by using the diffData() method around a CuffData, CuffGeneSet, or CuffGene object:

e.g.

myDiff<-diffData(genes(cuff))

Cheers,
Loyal
lgoff is offline   Reply With Quote
Old 05-06-2012, 04:49 PM   #11
billstevens
Senior Member
 
Location: Baltimore

Join Date: Mar 2012
Posts: 120
Default

How do you change the plotting parameters (title, x-axis, sample names, etc.) in csDensity? I tried to put it in the call, but that didn't work:

densityplot1 <- csDensity(genes(cuffy), xlab="xaxis")

When I then ran densityplot1, it didn't change the name of the x-axis.

I also tried just adjusting it after it plotted, but I kept getting an error saying plot.new has not been created.
billstevens is offline   Reply With Quote
Old 05-06-2012, 06:21 PM   #12
sdriscoll
I like code
 
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438
Default

They are using the ggplot2 package. I came across a short tutorial for it somewhere. You can't use they typical R options but you can edit the plots after they are generated. I don't remember the. Commands though. Google that package and look for their tutorial.
sdriscoll is offline   Reply With Quote
Old 05-07-2012, 05:39 PM   #13
lgoff
Member
 
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82
Default

Quote:
Originally Posted by sdriscoll View Post
I think in the log plots where they are plotting FPKM values they add 1 to the data. If you don't the density plot looks totally different.
Hi All, this is correct. In general when we have to log-transform, we add a pseudocount and we default to using '1'. When we do this however, we always add a 'pseudocount' argument that you can change to whatever value you would prefer to add.

Cheers
Loyal
lgoff is offline   Reply With Quote
Old 07-16-2012, 02:36 PM   #14
ftorri
Member
 
Location: Orange County

Join Date: Oct 2010
Posts: 11
Default

Hi,

I am trying to pull out from the scatter plot the list of the outliers, but I haven't found a way through. Does anyone of you have any suggestions?

Thanks!
Fed
ftorri is offline   Reply With Quote
Old 07-18-2012, 12:32 PM   #15
apadr007
Member
 
Location: washington DC

Join Date: Oct 2011
Posts: 21
Default

^ This would be helpful ^
apadr007 is offline   Reply With Quote
Old 01-25-2013, 08:36 AM   #16
nr23
Member
 
Location: Ireland

Join Date: Oct 2012
Posts: 42
Default

I'd love to know how to do this too!
nr23 is offline   Reply With Quote
Old 12-29-2016, 09:05 PM   #17
shahanasj21
Junior Member
 
Location: Kerala

Join Date: Dec 2016
Posts: 1
Default

Hi,
I have tried cummeRbund density graph after merging the two files. But in result i got 2 graphs... Could anyone explain the reason for this
shahanasj21 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:58 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO