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Difference between revisions of "Collect.shared"

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===jumble===
 
By default collect.shared will randomize the order of the sequence names in your group file. If you like the way the names are ordered in your group file, you can use the jumble option:
 
 
mothur > collect.shared(jumble=0)
 
  
  

Revision as of 14:35, 15 June 2009

The collect.shared command generates collector's curves for calculators, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling. mothur has the ability to generate data for collector's curves much the same way that sons did; however, sons presented the data in the sons file, which was virtually impossible for novices to parse. mothur fixes many of these issues by generating separate files for each estimator. For this tutorial you should download and decompress Patient70Data.zip


Default settings

To execute the collect.shared() command you first need to have either run the read.otu command with the list and group options. For example:

mothur > read.otu(list=patient70.fn.list, group=patient70.tissue_stool.groups)

By default, the collect.shared() command will randomize the order in which the individuals are sampled. So if you run collect.shared() multiple times, you will get slightly different results. The collector's curve data for several calculators is generated by default with the following command:

mothur > collect.shared()

This will result in output to the screen looking like:

unique	1
0.00	2
0.01	3
0.02	4
0.03	5
0.04	6
0.05	7
0.06	8
0.07	9
0.08	10
0.09	11
0.10	12

The left column indicates the label for each line in the data set and the right column indicates the row number in the data set. Execution of collect.shared() will generate 11 files, one for each of the calculators. If you look at patient70.fn.shared.sobs you will see something like:

sampled	uniquetissuestool	0.00tissuestool	0.01tissuestool	0.02tissuestool	0.03tissuestool
1	1			1		1		1		1
100	90			78		56		35		31
200	173			123		75		58		46
300	250			163		93		66		57
400	324			203		106		74		61
500	395			233		124		80		68
600	463			263		131		89		70
...

In this file the first column tells you how many sequences have been sampled; this would typically be plotted on the x-axis of a graph. Each subsequent column has a heading, which indicates the label for the line being analyzed from your OTU data file concatenate to the names of the two groups being compared. The data in the column provides the estimator value as indicated by the name of the file. For example, in the above examples, after sampling 600 sequences there were 463 OTUs shared between the tissue and stool samples when an OTU was defined as a group of identical sequences. By default, collect.shared() prints output every 100 sequences.


Options

calc

If you are not interested in producing collector's curves for all of the calculators, it is possible to select the calculators you want using the calc option:

mothur > collect.shared(calc=sobs-sharedchao)

This command would only generate the files patient70.fn.shared.sobs and patient70.fn.shared.chao.


line & label

There may only be a couple of lines in your OTU data that you are interested in generating collector's curves for. There are three options. You could: (i) manually delete the lines you aren't interested in from your list file; (ii) use the label option; and (iii) use the line option. To use the label option with the collect.shared() command you need to know the labels you are interested in. If you want the collector's curve data for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:

mothur > collect.shared(label=unique-0.03-0.05-0.10)

or

mothur > collect.shared(label=1-5-7-12)

In the file patient70.fn.shared.sobs you would see something like:

sampled	uniquetissuestool	0.03tissuestool	0.05tissuestool	0.10tissuestool	
1	1			1		1		1
100	92			26		24		16
200	179			39		34		24
300	258			51		38		27
400	332			57		47		29
500	404			64		49		29
600	473			67		51		31


freq

For larger datasets you might not be interested in obtaining all of the data for the number of sequences sampled. For instance, if you have 100,000 sequences, you may only want to output the data every 100 sequences. Alternatively, if you only have 100 sequences, you may only want to output all of the data. The default setting is to output data every 100 sequences. By altering the freq option you can set the frequency that the analysis is performed:

mothur > collect.shared(freq=1)

or

mothur > collect.shared(freq=1000)

The second command would generate data such as this in the patient70.fn.shared.sobs file:

sampled	uniquetissuestool	0.00tissuestool	0.01tissuestool	0.02tissuestool	0.03tissuestool	0.04tissuestool	0.05tissuestool		
1	1			1		1		1		1		1		1
1000	711			361		167		102		80		69		60
2000	1351			506		205		119		94		80		74
3000	1976			619		237		129		99		88		83
4000	2519			688		255		138		107		91		84
4392	2742			713		257		138		111		94		84



groups

If you had started this tutorial with the following comamnds:

mothur > read.otu(list=patient70.fn.list, group=patient70.sites.groups)
mothur > get.group()

You would have seen that there were 7 groups here: 70A-70F and 70S. The sequences from 70S were collected from Patient 70's stool sample those from samples 70A-70F were from their mucosa. These 7 groups would yield 21 pairwise comparisons if you ran the collect.shared command; however, if you were only interested in the comparisons between each mucosa site and the stool sample you could use the group option:

mothur > collect.shared(calc=sharedsobs, groups=70A-70S)
mothur > collect.shared(calc=sharedsobs, groups=70B-70S)
mothur > collect.shared(calc=sharedsobs, groups=70C-70S)
mothur > collect.shared(calc=sharedsobs, groups=70D-70S)

Alternatively, if you want all of the pairwise comparisons you can either not include the group option or set it equal to "all".

mothur > collect.shared(calc=sharedsobs, groups=all)