Create Venn plots from counts
Several Web-Tools exist to create Venn plots from the full categorized data (see Venn and other plots for a list) but little is available to just create the Venn diagrams from the final counts in each Venn region. The nice R-Bioconductor colorfulVennPlot [1] allows just this and was used to build simple scripts [2] that will turn your recall data into simple Venn plots.
[ Main_Page ]
Contents
CLI Venn scripts to plot recall analysis results
These scripts are meant for vizalization of summary counts obtained from CLI applications (e.g. intersect counts between several 'algorithm-X' runs of variant lists obtained by different callers or datasets).
Unlike other such tools, the scripts take the individual counts passed by command-line arguments to plot them in the corresponding Venn areas. The arguments allow some additional level of customization like generating white, grey, or colored backgrounds venn diagrams (run with -h for more details).
Requirements
In order to use these scripts, you will need [R] and RScript installed on your computer (done by most package installers including yum and apt-get).
You will also need the following three [R] packages:
- gridBase http://cran.r-project.org/web/packages/gridBase/ required for *colorfulVennPlot* plotting.
- colorfulVennPlot http://cran.r-project.org/web/packages/colorfulVennPlot/ to actually plot the Venn diagrams.
- optparse http://cran.r-project.org/web/packages/optparse/ to handle command line arguments.
Installing the dependencies is documented on the top of the code. Please read the respective package documentations if you wish to improve these scripts.
a 2-way Venn plot example
command line arguments
Options:
-a A.COUNT, --a.count=A.COUNT
counts for A-only
-b B.COUNT, --b.count=B.COUNT
counts for B-only
-i AB.COUNT, --ab.count=AB.COUNT
counts for AB-intersect
-A A.LABEL, --a.label=A.LABEL
label for A
-B B.LABEL, --b.label=B.LABEL
label for B
-t TITLE, --title=TITLE
Graph Title
-o FILE, --file=FILE
file name for output [default: 2Dvenn.png]
-u FILL, --fill=FILL
fill with 1:colors, 2:greys or 3:white [default: 3]
-h, --help
Show this help message and exit
eg: plots returned by the empty command ./2DVenn.R with the color option '-u 1', '-u 2', '-u 3 (default)'
 |
 |
 |
|---|
a 3-way Venn plot example
command line arguments
Options:
-a A.COUNT, --a.count=A.COUNT
counts for A-only
-b B.COUNT, --b.count=B.COUNT
counts for B-only
-c C.COUNT, --c.count=C.COUNT
counts for C-only
-d AB.COUNT, --ab.count=AB.COUNT
counts for AB-intersect
-e AC.COUNT, --ac.count=AC.COUNT
counts for AC-intersect
-f BC.COUNT, --bc.count=BC.COUNT
counts for BC-intersect
-i ABC.COUNT, --abc.count=ABC.COUNT
counts for ABC-intersect
-A A.LABEL, --a.label=A.LABEL
label for A
-B B.LABEL, --b.label=B.LABEL
label for B
-C C.LABEL, --c.label=C.LABEL
label for C
-t TITLE, --title=TITLE
Graph Title
-o FILE, --file=FILE
file name for output [default: 3Dvenn.png]
-u FILL, --fill=FILL
fill with 1:colors, 2:greys or 3:white [default: 3]
-h, --help
Show this help message and exit
eg: plots returned by the empty command ./2DVenn.R with the color option '-u 1', '-u 2', '-u 3 (default)'
 |
 |
 |
|---|
a 4-way Venn plot example
command line arguments
Options:
-a A.COUNT, --a.count=A.COUNT
counts for A-only [default: 0]
-b B.COUNT, --b.count=B.COUNT
counts for B-only [default: 0]
-c C.COUNT, --c.count=C.COUNT
counts for C-only [default: 0]
-d D.COUNT, --d.count=D.COUNT
counts for D-only [default: 0]
-e AB.COUNT, --ab.count=AB.COUNT
counts for AB-intersect [default: 0]
-f AC.COUNT, --ac.count=AC.COUNT
counts for ACB-intersect [default: 0]
-g AD.COUNT, --ad.count=AD.COUNT
counts for AD-intersect [default: 0]
-j BC.COUNT, --bc.count=BC.COUNT
counts for BC-intersect [default: 0]
-k BD.COUNT, --bd.count=BD.COUNT
counts for BD-intersect [default: 0]
-l CD.COUNT, --cd.count=CD.COUNT
counts for CD-intersect [default: 0]
-m ABC.COUNT, --abc.count=ABC.COUNT
counts for ABC-intersect [default: 0]
-n ABD.COUNT, --abd.count=ABD.COUNT
counts for ABD-intersect [default: 0]
-p ACD.COUNT, --acd.count=ACD.COUNT
counts for ACD-intersect [default: 0]
-q BCD.COUNT, --bcd.count=BCD.COUNT
counts for BCD-intersect [default: 0]
-i ABCD.COUNT, --abcd.count=ABCD.COUNT
counts for ABCD-intersect [default: 0]
-A A.LABEL, --a.label=A.LABEL
label for A [default: A]
-B B.LABEL, --b.label=B.LABEL
label for B [default: B]
-C C.LABEL, --c.label=C.LABEL
label for C [default: C]
-D D.LABEL, --d.label=D.LABEL
label for D [default: D]
-t TITLE, --title=TITLE
Graph Title [default: null]
-o FILE, --file=FILE
file name for output [default: 4Dvenn.png]
-u FILL, --fill=FILL
fill with 1:colors, 2:greys or 3:white [default: 3]
-h, --help
Show this help message and exit
eg: plots returned by the empty command ./2DVenn.R with the color option '-u 1', '-u 2', '-u 3 (default)'
 |
 |
 |
|---|
References:
[ Main_Page ]
