eVenn (version 2.1.6)

evenn: eVenn: A powerful to quickly compare huge lists and draw Venn diagrams.

Description

Compute a matrix comparison of lists (from 2 to infinite) and plot the results in a Venn diagram if (N

Usage

evenn(annot = FALSE, matLists="", path_res = "", path_lists = "", res = "", ud = FALSE, prop=FALSE, noms="", overlaps=FALSE, f=0, display=FALSE, couleurs="", FilesOut=TRUE, CompName="")

Arguments

annot

If the lists to be compared are files with identifiers (used for comparisons) and data (annotations or whatever). The identifiers data (Gene name and extended name) must be the 2nd and 3rd columns.

matLists

To use eVenn on matrix instead of text files. The "noms" variable must be used to give names to the compared matrix / lists

path_res

Path used to save the results. The working directory is used by default.

path_lists

Path used to find the lists to be compared. There is no default. The files must be text tabulated or csv format.

res

Binary matrix showing which identifier belong to which lists. Columns are compared lists, rows are identifiers.

ud

If the details of up and down regulated genes should be shown. Then the source files must comport a "ratios" column.

prop

If the surfaces of the disks should be proportional to the size of the lists.

noms

Cutom short names for each list, used in the 4 lists venn with ud details.

overlaps

Compute the overlaping proportions for each couple of lists in two ways (A in B and B in A). A heatmap is created if at least three lists are processed.

f

Set a minimum overlap to produce a filtered overlaps matrix. Default f=0 is set to no filter.

display

Draw a title in ascii art.

couleurs

Vector of custom colours to be used in the graphics. Default colours: c("blue", "red", "green", "orange")

FilesOut

For use of eVenn without producing files but only return a results binary matrix. (results = evenn())

CompName

Name of the folder results.

Value

• All the results are saved in a folder names with date and hour. The comparison bunary matrix is saved as a csv file "venn_matrix.csv". If annot is True, the resulting file (same as venn matrix with annotation given by the source lists) is saved as a text file "venn_annot.txt". The venn diagram is saved in a pdf file "venn_diagram.pdf". The venn diagram with up/down informations is saved in a pdf file "venn_diagram_ud.pdf".

References

http://blog.mrbioinfo.com/

Examples

#exemple with 2 lists
data(res2)
evenn(path_lists="test", res=res2, ud=TRUE)

#exemple with 3 lists
data(res3)
evenn(path_lists="test", res=res3, ud=TRUE)

#exemple with 4 lists
data(res4)
evenn(path_lists="test", res=res4, ud=TRUE)