autoevenn: Automates the process of several eVenn
In eVenn: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn Diagrams

Description Usage Arguments Author(s) References

View source: R/autoevenn.R

This function creates a list of folders where are placed sources files for venn diagrams and call the eVenn function for each one.

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).