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Indicator

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The indicator command can be run in 3 ways: with a shared or relabund file and a design file, or with a shared or relabund file and a tree file, or with a shared or relabund file, tree file and design file. The indicator command outputs a .indicator.summary file and a .indicator.tre if a tree is given. The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file. The summary file lists the indicator value for each OTU for each node. To run this tutorial please download JCZData.zip.


For background on the indicator metric, see:

Dufrene M, Legendre P (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345-66.

McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR.

Legendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York.


Default Settings

First let's run the indicator command with a tree and shared file:

mothur > indicator(tree=jcz.tx.morisitahorn.1.tre, shared=jcz.tx.shared)
You did not provide a label, I will use the first label in your inputfile.

Node	Species	IndicatorValue	pValue
121	OTU15	99.447250	0.028000
121	OTU44	91.346153	0.043000
121	OTU56	98.901100	0.039000
121	OTU60	77.068680	0.039000
121	OTU89	100.000000	0.049000
121	OTU105	100.000000	0.048000
121	OTU115	100.000000	0.048000
121	OTU132	98.275856	0.048000
122	OTU2	76.412704	0.002000
122	OTU3	45.613029	0.012000
122	OTU7	59.255600	0.008000
122	OTU8	64.915779	0.015000
122	OTU9	79.820976	0.003000
122	OTU11	48.265816	0.024000
122	OTU14	93.424797	<0.001000
...

mothur will output any OTU with a pValue <= 0.05 for each tree node. All values are reported in the .indicator.summary file.


Now let's run it with a shared, tree and design file. When using a design file the tree file should represent how the groupings relate to each other.

mothur > indicator(tree=jcz.tx.merge.morisitahorn.1.tre, shared=jcz.tx.shared, design=jcz.design)
You did not provide a label, I will use the first label in your inputfile.

Node	Species	IndicatorValue	pValue
7	OTU2	38.001118	0.009000
7	OTU3	37.174728	0.012000
7	OTU5	37.466076	0.010000
7	OTU7	41.481815	0.013000
7	OTU10	47.395081	0.005000
7	OTU11	44.400589	0.012000
7	OTU13	49.684628	0.004000
7	OTU14	28.282827	0.036000
...

Lastly, you can run the indicator command with a shared and design file.

mothur > indicator(shared=stool.final.an.shared, design=stool.design)
Species	IndicatorValue	pValue
OTU1	93.969849	<0.001000
OTU3	100.000000	<0.001000
OTU4	64.899826	0.035000
OTU8	63.636364	0.017000
OTU9	72.727272	0.011000
OTU10	67.565987	0.032000
OTU11	81.570129	0.006000
OTU12	64.149368	0.024000
OTU14	54.545456	0.029000
OTU18	70.831558	0.040000
OTU22	66.666672	0.013000
OTU33	63.636364	0.019000
OTU35	70.329437	0.040000
OTU36	83.856499	0.005000
OTU40	53.582375	0.035000
OTU57	70.576378	0.020000
OTU64	66.754623	0.047000
OTU67	69.847153	0.020000
OTU85	74.171631	0.015000
OTU97	61.197342	0.027000
OTU122	56.617649	0.044000
OTU124	63.636364	0.019000
OTU130	67.622948	0.023000
OTU163	45.454548	0.046000
OTU177	90.909096	<0.001000
OTU198	66.000000	0.018000
OTU200	63.636364	0.020000
OTU206	50.000000	0.041000
OTU213	70.512817	0.007000
OTU223	50.000000	0.032000
OTU254	66.666672	0.012000
OTU278	50.000000	0.038000
OTU401	50.000000	0.049000
OTU524	53.070175	0.039000


It took 92 secs to find the indicator species.


Options

iters

The iters parameter allows you to set number of randomization for the P value. The default is 1000.

 mothur > indicator(shared=stool.final.an.shared, design=stool.design, iters=10000) 

processors

The processors option allows you to speed up the processing time.

 mothur > indicator(shared=stool.final.an.shared, design=stool.design, processors=2)

groups

The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed. The groups may be entered separated by dashes.

mothur > indicator(tree=jcz.tx.morisitahorn.1.tre, shared=jcz.tx.shared, groups=P3S9-M3S3-M3S6-P3S5-P1S4-M2S10-M1S19-P3S15)

label

The label parameter indicates at what distance your tree relates to the shared or relabund. If label is not provided, then the first label in the shared or relabund file will be used.

 mothur > indicator(tree=jcz.tx.morisitahorn.1.tre, shared=jcz.tx.shared, label=1)

design

The design file is used to group your groups. It looks just like a group_file, but the first column contains group names and the second column contains the grouping that the group belongs to. When using a design file the tree file should represent how the groupings relate to each other.

mothur > indicator(tree=jcz.tx.merge.morisitahorn.1.tre, shared=jcz.tx.shared, design=jcz.design)