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Tuesday 20 March 2012

eVenn V2.1.5

       In this new version I have added the possibility to use eVenn like a simple function by giving a list of matrixes in input to get a binary matrix in output.
       The eVenn v2.1.5 package is available at the CRAN website.



Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-gcc-debian 2.1.5 1.29 21.08 22.37 OK
r-devel-linux-x86_64-gcc-fedora 2.1.5 21.60 OK
r-prerel-linux-x86_64 2.1.5 1.22 21.18 22.40 OK
r-prerel-solaris-sparc 2.1.5 143.10 OK
r-prerel-solaris-x86 2.1.5 31.00 OK
r-prerel-windows-ix86+x86_64 2.1.5 2.00 32.00 34.00 OK
r-release-linux-ix86 2.1.5 1.09 19.59 20.68 OK
r-release-macosx-ix86 2.1.5 1.00 21.00 22.00 OK
r-release-windows-ix86+x86_64 2.1.5 2.00 26.00 28.00 OK

Friday 15 July 2011

My tweet cloud.

Go to Nicolas Cagnard's Mirror.Me Reflection

Friday 13 May 2011

eVenn v2.1 do proportional venn diagrams.

eVennv2.1

       This new version corrects some bugs thanks to users who send me feedback of their problems and whishes. I have also added a new function: it draws proportional venn diagrams up to 4 compared lists. I had to make choices in the design of the proportional diagrams. The main choice was about the shape of the overlapping areas. The surfaces of the main circles are directly proportional to the size of the compared lists. The overlapping areas surfaces must be proportional to the number of common ID. Should I draw two overlapping circles or two separate circles with an additional circle sized to the overlapping list?

OverlappRepresentationMethods

       I think it is easier to compare different sizes of the same shape (B) than surfaces with different shapes (A), so I have chosen to give priority to the clarity and ease of understanding. The main problem was to find a logical order for the multiple circles and make easy to depict their connections. I haven’t found any logical coloring code for the secondary circles so I have only colored the main circles and let the other in black. In spite of coloring the circles I had drawn colored connections to highlight and make easy to know which lists are associated to which overlap circle.

PropVenn2
PropVenn3
PropVenn4

       Some problems could happen with the text size for very small lists or very huge lists; I am working on a potential solution. The R package will be available soon.


CRAN page of eVenn 2.1

CRAN checks for eVenn results:

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-ix86 2.1 0.96 17.26 18.22 NOTE
r-devel-linux-x86_64-gcc-debian 2.1 1.20 21.27 22.47 NOTE
r-devel-linux-x86_64-gcc-fedora 2.1 21.13 OK
r-patched-linux-ix86 2.1 0.95 17.71 18.66 NOTE
r-patched-linux-x86_64 2.1 0.95 20.99 21.94 NOTE
r-patched-solaris-sparc 2.1 146.80 OK
r-patched-solaris-x86 2.1 27.90 OK
r-patched-windows-ix86+x86_64 2.1 3.00 67.00 70.00 OK
r-release-linux-ix86 2.1 1.08 20.11 21.19 NOTE
r-release-macosx-ix86 2.1 1.00 21.00 22.00 OK
r-oldrel-macosx-ix86 2.1 1.00 21.00 22.00 OK
r-oldrel-windows-ix86+x86_64 2.1 1.00 29.00 30.00 OK

Tuesday 15 February 2011

eVenn v1.30 is out!

This new version adds a new function to compute the overlaps proportions of each combination in the two ways.
The classical Venn diagram computes only the sizes of overlaps like numbers of genes, probes or IDs (A). But sometimes we need to know which are the proportions of the overlaps for each of the compared lists (B).
The Overlap function allows computing a table of overlaps (C). In this example the overlap of A in B is about 33% whereas the overlap of B in A is about 20%.


To know the overlap proportion of A in B you just have to choose the line of A (overlapping) and the column of B (reference) (D).


A heat map from the produced matrix of overlaps allows an overview of the results.


The note of the CRAN Package Check will be solved in the next version (v1.31) available soon this week.

Wednesday 22 December 2010

AnnotLists v1.0

This new package AnnotLists uses the core function of eVenn in a derivate way.

The eVenn core function priciple is to find in a matrix all the related data to a list of identifier.


AnnotLists uses this principle to find data in a matrix B related to the data in the matrix A using common identifiers.


The first list or matrix ("list") is used as the reference, each identifier will be used to find data in the second list or matrix ("Annotations").
1: The matrix B is the reference, so it is used as a filter for the data of the B matrix. The filter is to only select the data in A where ID from B = ID from A.
2: In this example the A data matrix is used as the reference to find corresponding data in the B matrix.



CRAN package AnnotLists


Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-gcc-fedora 1.0

9.99 OK
r-patched-solaris-sparc 1.0

76.30 OK
r-patched-solaris-x86 1.0

17.30 OK
r-release-windows-ix86+x86_64 1.0 1.00 16.00 17.00 OK
r-oldrel-windows-ix86 1.0 4.00 19.00 23.00 OK

Thursday 16 December 2010

The eVenn core algorithm

Each time you need to retrieve information in a matrix starting of data from another matrix or list you should do a matrix comparison instead of doing an iterative research. You are confronted to the same problem for things really useful like finding annotations from a large identifiers list.
The time used is proportional to the sizes of the compared matrix.
The principle is really simple and could be used in many cases so I will expose and comment the core algorithm I have used in eVenn.

In this example I will use only two short lists.
The result will be a “res” binary matrix with one line for each identifier and one column for each list (1 if the identifier belongs to a list, 0 if not).


- The “res” matrix is initiated with the first where all the identifiers belong to. The identifiers are the names of the lines.


- (1) The first step is to read a second list and use the “duplicated” function. If the “res” identifiers (row names) list is concatenated at the end of the second list you will highlight the new identifiers belonging to the second list but not to the first. If the second list is concatenated to the first, the “old” identifiers specifics of the previous lists are highlighted.

- (2) If new identifiers are detected they are added to the “res” matrix. The column(s) are filled with “0” because this new identifiers don’t belongs to the previous list(s).

- (3) A new one column matrix is created independently, concatenating the “old” identifiers (associated with “0”) and the current compared list (associated with “1”).

- (4) The new matrix then is ordered and concatenated to the “res” matrix. 

Friday 12 November 2010

eVenn 1.24 is OK in every CRAN flavors !

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-ix86 1.24 0.44 10.55 10.99 OK
r-devel-linux-x86_64-gcc-debian 1.24 0.50 11.88 12.38 OK
r-devel-linux-x86_64-gcc-fedora 1.24

13.96 OK
r-patched-linux-ix86 1.24 0.45 10.50 10.95 OK
r-patched-linux-x86_64 1.24 0.51 11.99 12.50 OK
r-patched-solaris-sparc 1.24

103.00 OK
r-patched-solaris-x86 1.24

21.90 OK
r-release-linux-ix86 1.24 0.54 11.32 11.86 OK
r-release-windows-ix86+x86_64 1.24 5.00 22.00 27.00 OK
r-prerel-macosx-ix86 1.24 6.00 19.00 25.00 OK
r-oldrel-windows-ix86 1.24 2.00 24.00 26.00 OK

Tuesday 9 November 2010

eVenn v1.24


       A man() function have been added to the package. It gives you a quick help with usefull informations and details on the main variables to start using the function.

       Now if you do not remember the function prototype to make a quick venn diagram, you just have to check the man() and a copy/paste !


       I have also worked on the design of the graphics to improve the definition, letters aligment, etc..

       In this version you can customize the "4 lists Venn diagram" with short names for your lists. Deafualt short names are "A", "B", "C", "D".




Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-ix86 1.23 0.43 10.65 11.08 OK
r-devel-linux-x86_64-gcc-debian 1.23 0.51 12.09 12.60 OK
r-devel-linux-x86_64-gcc-fedora 1.24

14.31 OK
r-patched-linux-ix86 1.23 0.43 10.72 11.15 OK
r-patched-linux-x86_64 1.23 0.53 12.23 12.76 OK
r-patched-solaris-sparc 1.24

103.00 OK
r-patched-solaris-x86 1.24

24.60 OK
r-release-linux-ix86 1.23 0.55 11.41 11.96 OK
r-release-windows-ix86+x86_64 1.24 5.00 22.00 27.00 OK
r-prerel-macosx-ix86 1.24 6.00 19.00 25.00 OK
r-oldrel-windows-ix86 1.24 2.00 24.00 26.00 OK

Saturday 16 October 2010

Coulds comparison v0.1

       A problem has been submitted to me last evening, so it became my little headache for the weekend! I am not shure of my solutions...
       It is about comparaison of two clouds of points, like I use to do with samples comparisons but with a supplemental dimension. The datas are two lists of points with x and y coordinates.
       In this graph the clouds seems to be completely overlapped, the points in bold are the barycenters.
       I have drawn the barycenter line because my first idea was to reduce the dimensions by orthogonal projection. I have took the coordinates of each points orthogonaly projecter on the barycenter line and compute the distances from a common reference (the pont projected with the min (x)). There must be a bug in my script or in the graph because the projections are clearly not orthogonal... I need time to work on that problem.
       The result is two lists of distances that I can test by a classical Student...

       This density graph show the relative distributions of the two mesures populations, computed from the two clouds. The dark lines are the means and the ligts are the mean+/-2sd.The Student pval is in the title of the graph.

       This method do not take account of the 2D dispersion of the clouds so I have also used the distances to the barycenters instead of the orthogonal projections (this methode is way more simple but this idea has took time to come...).
       This method produces very different values and the variabilities of the clouds seems to be preserved.
       This density graph show the relative distributions of the distances from the barycenters.
       The script, the data sources and the figures are here.

Tuesday 14 September 2010

eVenn v1.22 is online

       This new version is just a minor update with some minor bug corrections before a real new version which will try to manage and prevent errors of option choice.

eVenn v1.22

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-ix86 1.21 0.43 9.79 10.22 OK
r-devel-linux-x86_64-gcc-debian 1.21 0.48 11.44 11.92 OK
r-devel-linux-x86_64-gcc-fedora 1.21

13.64 OK
r-devel-windows-ix86+x86_64 1.22 1.00 22.00 23.00 OK
r-patched-linux-ix86 1.21 0.42 10.80 11.22 OK
r-patched-linux-x86_64 1.21 0.47 11.12 11.59 OK
r-patched-solaris-sparc 1.22

103.40 OK
r-patched-solaris-x86 1.22

18.40 OK
r-patched-windows-ix86 1.22 4.00 22.00 26.00 OK
r-patched-windows64-x86_64 1.22 2.00 21.00 23.00 OK
r-release-linux-ix86 1.21 0.52 12.00 12.52 OK
r-release-macosx-ix86 1.21 1.00 13.00 14.00 OK

Saturday 11 September 2010

My meta analysis method is in Immunity !

The solved problem for which I have used a really simple meta analysis method is now online in "Online Ahead of Issue" of the Immunity journal.

The method is quickly described in the article: Human CD14dim Monocytes Patrol and Sense Nucleic Acids and Viruses via TLR7 and TLR8 Receptors





This is the first published scientific artcile using my script, I am currently working on another but it will take some times before published.

I will maiby make an R package but for now this is juste a simple script.

Monday 9 August 2010

Auto Shift Circles Plot

       There are many types of plots scripts available but this one have something different which hade been very funny to code.

       The main principle is to drow a circle plot of two data sets which are statistically compared by Man Whitney and Student tests.

       The circles are drawn from down to up whith progressing shift to the left to avoid overlap This method is adjusted if the circle diameter is changed.

       If you want to use the same scale for a serie of graphics you have to put identical name before the "_" in the name of the lines (as it'd done in the data set example for times series).


       The script and an example data set.

Thursday 29 July 2010

Meta analysis without limits !

       I have met a "new exciting bioinformatics’ problem" ! This time it is about limits of meta-analysis and because I dived inside 24/7, it is about transcriptomics! Is there a method which allows comparing any dataset to any other? Without limitations with neither species nor micrroarray types nor any other traditional biais we spend so much time to avoid...?

A simple problem

       To illustrate I have drawn a scheme of the real problem on which I have spend some nights: two data sets of microarrays analysing feww cell lines  from two different species.


Nicolas Cagnard MetAnalyze

       Each group set is a microarrays of biological triplicates for a cell line.

       In one specie all the cell lines have been well characterized, maybe because it’s way easy to work on mice than in humans.

       The goal is to identify the cell type’s correspondences throughout the species. The well characterized cell lines in the two species are the true positives, the unknown are the challenging and exciting bioinformatics’ problem.

       I think that I have found a really simple solution which works pretty well but I have to wait for reviewers.

       One day I will post here my solution... Maybe soon, maybe not.

Saturday 17 July 2010

eVenn v1.2 is in the place !

       eVenn v1.1 was able to compare infinite number of lists, to make venn diagrams of four listes and create comparison annotated matrix.

       The most part of my job is about transcriptomic projects, so I frequently need to compare lists of regulated genes or probes with fold change information.

       The version 1.2 of eVenn is able to show the details of regulation profiles in venn diagrams.

       To use this new function a new variable "ud" is needs to be TRUE and all the lists to be compared must comport a "ratios" column.

       "annot" and "ud" are independant variables.

       The results of a comparion of four lists with taking account of the ratios is like that:



       There was no enougth place inside the graph to write all the potential profiles (2^number of compared lists) so I have used the space around trying to not cross the profils lists. I have also reduced the police size.

       I hope the colours help to quickly understand which is where.

       The packages have been sent to the CRAN repository today. Windows version, Linux version, annotated source file (french).

Thursday 8 July 2010

FcFc plot v0.3 rocks !

       Here is the script I was talking about in a this post.

       The data souce file must be a tab separated text file with two columns, each for the fold change lists you want to compare. The first column will be ploted on the X-axis, the second on the Y-axis. Fold change must not be logged. The axis names takes the two columns names of your source file.

       Three options are avilable:

              - fold is to fix the filtration limit on folds.

              - listes if you want to have the lists of genes/probes specifis for each graphic regions.

              - annot if you want to have annotated filtred lists.




Wednesday 7 July 2010

eVenn V1.1

       The last version of eVenn is on his way  to CRAN.
       This new version do not longer use external package (plotrix) and allow to compare either annotated listes and list with just one column (=> IDs).
       eVenn v1.1 package tar.gz version.      
       eVenn v1.1 package zip version.     



Saturday 3 July 2010

NOTE in the Check of GExMap

       I am looking to solve this note problem but it has absolutely no influence on the results neither the run of the script .

                    checking R code for possible problems ... NOTE
                    gexload.corr: no visible binding for global variable ‘corr’

     It seems to be about a variable which is only created and used inside the gexload.corr function but not mentioned in the man file...

CRAN Package Check Results for Package GExMap

Last updated on 2010-07-03 11:54:43.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-ix86 1.1 1.89 107.79 109.68 NOTE
r-devel-linux-x86_64-gcc-debian 1.1 2.03 130.06 132.09 NOTE
r-devel-linux-x86_64-gcc-fedora 1.1

194.18 NOTE
r-patched-linux-ix86 1.1 2.04 109.49 111.53 NOTE
r-patched-linux-x86_64 1.1 2.08 127.66 129.74 NOTE
r-patched-solaris-sparc 1.1

871.90 NOTE
r-patched-solaris-x86 1.1

205.40 NOTE
r-release-linux-ix86 1.1 2.14 104.86 107.00 NOTE
r-release-macosx-ix86 1.1 4.00 156.00 160.00 NOTE
r-release-windows-ix86 1.1 4.00 149.00 153.00 NOTE
r-release-windows64-x86_64 1.1 14.00 197.00 211.00 NOTE
r-oldrel-macosx-ix86 1.1 2.00 111.00 113.00 NOTE
r-oldrel-windows-ix86 1.1 16.00 223.00 239.00 NOTE

Wednesday 30 June 2010

FcFc graphs in R

       I'm working on adding a new type of graphic in the futur "graph package" which will be my favourite toolbox.

       I frequently need to produce several types of graphics starting from gene lists mostly coming from microarray analysis.

       Mains problems are to find the good package, understand in which format the data has to be, format it (what a time expensive step !) and finaly fight with multiples options to have the good shapes and colours.

       The goal of my graphics-toolbox is to make graphics easily and quickly starting from simple text files.

       Today I will add the FcFc plot which allows to compare the fold changes of two differntially expressed lists.

       The result is a log2 scatter plot where relevant groups are coloured.




       I will post here the source file as soon as it is functional.

Monday 28 June 2010

Packages in CRAN for R version 2.11.1 (2010-05-31) (32-bit)

       The new versions of my packages are only available in the R 2.11.1 folder but they work on previous versions of R.

              - eVenn v1.01
              - GExMap v1.1

       I am working on a new version of eVenn which do not use external package (as plotrix) and new packages (one make easy to produce several graphics types and another to introduce a meta analysis methode I frequently use.)

Friday 18 June 2010

eVenn V1.01

      Here comes a new version of the eVenn package !

      I already had suggestions of users about the supported file types. This new version accept the txt/tabulation files but also the csv files (";" and "," separator). A function tests the type and separator type before reading each file. You can now use different file-types in the same run. If the file type is unknown and so unsupported there is now a specific error message.



      The new version have been subbmited to the R-project. Windows version (zip), Linux version (tar.gz).

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