Description Usage Arguments Author(s) References
This function creates a list of folders where are placed sources files for venn diagrams and call the eVenn function for each one.
1 2 3 4 | autoevenn(FolderPath="", pathRes="", annot=TRUE, ud=TRUE, prop=FALSE, overlaps=FALSE,
display=FALSE, couleurs="", VennBar=FALSE, transp=0.5, filled=TRUE, Profils=FALSE,
ColorTxt="", colBlack=FALSE, Ptest=FALSE, tUD=NULL, tUDp=NULL, tnoUD=NULL,
Gtype="png", lw=1, NutShell=TRUE, VennClust=TRUE, OnlyVenn=FALSE)
|
FolderPath |
Path where are placed the source data folders. |
pathRes |
Path used to save the results. The working directory is used by default. |
annot |
If the compared files got more than one column (not only IDs). |
ud |
If the source files comport a ratio or fold column the details of up and down regulated genes will be shown. |
prop |
If the surfaces of the disks should be proportional to the size of the lists. |
overlaps |
Compute the proportions of the overlaps 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. |
display |
Print commentaries during the process. |
couleurs |
Vector of custom colours to be used in the graphics. Default colours: c("blue", "red", "green", "orange") |
VennBar |
Represent the zones of a venn diagram with a bars chart even for more than 4 lists. |
transp |
Percentage of transparency of the disks. |
filled |
No transparancy, disks are filled with solid colours. |
Profils |
This option is valid only if the modulations (UD) are available (ie ratio column or each list) and a DataMoy.txt file containing the means of each group for all the items. The items will be separated by modulations profiles. |
colBlack |
No color, only Black on a white background. |
ColorTxt |
Custom color of the counts. |
Ptest |
Proportional test (Fisher's exact) of the non null areas. |
tUD |
Font size of the count and profile names of specific zones. |
tUDp |
Font size of the count and profile names of common zones. |
tnoUD |
Font size of the total count of a zone. |
Gtype |
File format of the graphic (png or svg). |
lw |
Line width relative to the default (default=1). 2 is twice as wide. |
NutShell |
All the Venn zones and UD profiles in a nutshell (count table). |
VennClust |
Creates two clusterings (using Spearman correlation similarity measure and average or Ward.D2 linkage algorithm) to model links between the lists. |
OnlyVenn |
Draw only the venn diagram without any text outside (remove the total and lists names). |
Author & Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.