Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

  • #2
    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

    Comment


    • #3
      Thanks for the answer, I understand now.

      Looking forward for the cookbook recipes.

      Comment


      • #4
        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,

        Comment


        • #5
          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

          Comment


          • #6
            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.

            Comment


            • #7
              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?

              Comment


              • #8
                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.
                /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
                Salk Institute for Biological Studies, La Jolla, CA, USA */

                Comment


                • #9
                  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

                  Comment


                  • #10
                    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

                    Comment


                    • #11
                      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.

                      Comment


                      • #12
                        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.
                        /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
                        Salk Institute for Biological Studies, La Jolla, CA, USA */

                        Comment


                        • #13
                          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

                          Comment


                          • #14
                            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

                            Comment


                            • #15
                              ^ This would be helpful ^

                              Comment

                              Latest Articles

                              Collapse

                              • seqadmin
                                Best Practices for Single-Cell Sequencing Analysis
                                by seqadmin



                                While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
                                06-06-2024, 07:15 AM
                              • seqadmin
                                Latest Developments in Precision Medicine
                                by seqadmin



                                Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

                                Somatic Genomics
                                “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
                                05-24-2024, 01:16 PM

                              ad_right_rmr

                              Collapse

                              News

                              Collapse

                              Topics Statistics Last Post
                              Started by seqadmin, Today, 08:58 AM
                              0 responses
                              8 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, Yesterday, 02:20 PM
                              0 responses
                              14 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 06-07-2024, 06:58 AM
                              0 responses
                              181 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 06-06-2024, 08:18 AM
                              0 responses
                              231 views
                              0 likes
                              Last Post seqadmin  
                              Working...
                              X