venn
The venn command generates a Venn diagram from data provided in a *.shared file. The command can generate diagrams (as SVG files) to compare the richness shared among 2, 3, or 4 groups. The SVG file that can be further modified in a program like Gimp or Adobe Illustrator to scale the areas to be proportional to the richness represented by the region. Options are available to measure richness based on the observed richness or the estimated richness using the chao and sharedchao calculators. This tutorial uses the data files in AbRecovery.zip.
Default settings
To execute venn(), shared data created:
mothur > cluster(phylip=abrecovery.dist, cutoff=0.10)
mothur > make.shared(list=abrecovery.fn.list, group=abrecovery.groups)
mothur > venn(shared=abrecovery.fn.shared)
This will generate 12 SVG files - a venn diagram for each OTU definition between unique and 0.10 (because of the cutoff in the read.dist command). For example, the venn diagram that is generated for OTUs defined at the 0.10 level would be abrecovery.fn.0.10.venn.sobs.svg.
Options
calc
By default the venn() command will calculate the shared richness based on the observed OTUs. Alternatively, it is possible to use the chao and sharedchao or the ace and sharedace calculators to predict the richness of each region. This option can be implemented by the following command:
mothur > venn(shared=abrecovery.fn.shared, calc=sharedchao)
Alternatively the observed richness can be used with the command:
mothur > venn(shared=abrecovery.fn.shared, calc=sharedsobs)
Both can be run simultaneously by the command:
mothur > venn(shared=abrecovery.fn.shared, calc=sharedsobs-sharedchao)
label
There may only be a couple of lines in your OTU data that you are interested in generating a venn diagram for. There are two options. You could: (i) manually delete the lines you aren’t interested in from you list or shared file; (ii) or use the label option. If you only want to read in the data for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:
mothur > venn(shared=abrecovery.fn.shared, label=unique-0.03-0.05-0.10)
group
At this point, if you run the following command:
mothur > get.group(shared=abrecovery.fn.shared)
You would have seen that there were 3 groups here: A, B, and C. If you just want the venn diagrams between groups A and B, A and C, or B and C enter the following:
mothur > venn(shared=abrecovery.fn.shared, groups=A-B)
mothur > venn(shared=abrecovery.fn.shared, groups=A-C)
mothur > venn(shared=abrecovery.fn.shared, groups=B-C)
Note that if you run these commands, the SVG files will have the same name and will be written over for each execution. You will need to rename the file between executions.
nseqs
The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.
mothur > venn(shared=abrecovery.fn.shared, nseqs=T)
permute
If you have more than four groups and set permute=t, mothur will create pictures with all possible 4-way permutations. The permute option can also be set to 1,2,3, or 4 to create combinations of varying size.
mothur > venn(shared=abrecovery.fn.shared, permute=t)
fontsize
The fontsize parameter allows you to adjust the fontsize in the picture mothur creates. The default is 24.
sharedotus
The sharedotus parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=t.
mothur > venn(shared=abrecovery.fn.shared, label=0.03)
The abrecovery.fn.0.03.sharedsobs.sharedotus file contains:
Groups NumShared OTULabels
A-B 15 Otu001,Otu003,Otu005,Otu007,Otu011,Otu012,Otu013,Otu014,Otu015,Otu026,Otu028,Otu030,Otu032,Otu040,Otu041
A-C 8 Otu008,Otu014,Otu023,Otu027,Otu030,Otu031,Otu032,Otu040
B-C 6 Otu014,Otu030,Otu032,Otu040,Otu044,Otu048
A-B-C 4 Otu014,Otu030,Otu032,Otu040
Why do the venn diagram results vary from get.sharedseqs results?
Confusion can occur when you have a shared file with more groups than just the subset you are looking at in your venn diagram. For this example let’s look at a simple shared file like:
Full shared file:
label group numOtus Otu001 Otu002 Otu003 Otu004 Otu005
0.26 A 5 43 38 2 0 1
0.26 B 5 46 14 10 13 1
0.26 C 5 16 29 29 0 0
mothur > venn(groups=B-C)
Venn shared file with groups B and C selected:
label group numOtus Otu001 Otu002 Otu003 Otu004 Otu005
0.26 B 5 46 14 10 13 1
0.26 C 5 16 29 29 0 0
C = 0 unique OTUs
B = 2 unique OTUs
BC = 3 shared OTUs
mothur > get.sharedseqs(uniquegroups=B)
Get.sharedseqs with uniquegroups=B shared file:
label group numOtus Otu001 Otu002 Otu003 Otu004 Otu005
0.26 A 5 43 38 2 0 1
0.26 B 5 46 14 10 13 1
0.26 C 5 16 29 29 0 0
B = 1 unique OTUs
The difference between the two commands is the groups mothur is considering when finding the unique and shared OTUs. With the venn command, mothur only uses the groups provided by the groups parameter or if none are provided the first 4 groups in the file. This is done because there are limits to the drawing of the venn diagram. With more than 4 groups the picture becomes too complicated to be of use. In this example group A is not included which changes the shared and unique composition.The get.sharedseqs command does not have the limitations of the picture. You can set parameters with the sharedgroups and uniquegroups. The sharedgroups parameter means the OTUs MUST include the groups you listed, but MAY also include other groups. The uniquegroups parameter means the OTUs MUST include the groups you listed and ONLY the groups you listed.
For example:
mothur > get.sharedseqs(uniquegroups=B-C)
B-C = 0 unique OTUs (no Otus contains just sequences from B and C)
mothur > get.sharedseqs(sharedgroups=B-C)
B-C = 3 shared OTUs (3 Otus contains sequences from B and C and sequences from other groups)
Revisions
- 1.23.0 - Added fontsize parameter.
- 1.29.0 - Added the sharedotus parameter.
- 1.29.1 - Bug Fix: segfault when no shared otus.
- 1.33.0 - permute parameter can equal 1, 2, 3, 4 or true. - https://forum.mothur.org/viewtopic.php?f=3&t=2629&p=7252#p7252
- 1.33.0 - Bug Fix: overwrote .sharedotu files when permute=t
- 1.40.0 - Speed and memory improvements for shared files. #357 , #347