We will be offering mothur and R workshops throughout 2019. Learn more.

Indicator

From mothur
Revision as of 15:40, 29 March 2018 by Westcott (Talk | contribs) (Revisions)

Jump to: navigation, search

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	Indicator_Groups	IndicatorValue	pValue
121	Otu015	M1S2	99.447250	0.026000
121	Otu044	M2S13	91.346153	0.047000
121	Otu054	M2S13	88.144333	0.041000
121	Otu056	M2S13	98.901100	0.038000
121	Otu060	M2S13	77.068680	0.035000
121	Otu073	M2S13	88.888893	0.047000
121	Otu089	P2S4	100.000000	0.045000
121	Otu139	M2S13	100.000000	0.048000
121	Otu148	M2S13	100.000000	0.048000
122	Otu002	P1S11-P1S18-P1S19-P1S20-P1S5	76.412704	0.003000
122	Otu003	P2S18-P2S19-P2S20-P3S8	45.613029	0.011000
122	Otu007	P2S1-P2S2-P2S3-P2S4	59.255600	<0.001000
122	Otu008	M3S3-M3S6-P3S9	64.915779	0.020000
122	Otu009	M3S10-M3S11-M3S12-M3S9	79.820976	0.004000
122	Otu011	P1S12-P3S1	48.265816	0.024000
122	Otu014	M3S10-M3S11-M3S12-M3S9	93.424797	0.002000
...

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	Indicator_Groups	IndicatorValue	pValue
7	Otu002	M3S12-M3S2-M3S3-M3S4-M3S5-M3S6-M3S7-M3S8-M3S9-P1S1-P1S10-P1S11-P1S12-P1S13-P1S14-P1S15-P1S16-P1S17-P1S18-P1S19	38.001118	0.022000
7	Otu003	P1S2-P1S20-P1S3-P1S4-P1S5-P1S6-P1S7-P1S8-P1S9-P2S1-P2S10-P2S11-P2S12-P2S13-P2S14-P2S15-P2S16-P2S17-P2S18-P2S19	37.174728	0.012000
7	Otu005	M3S12-M3S2-M3S3-M3S4-M3S5-M3S6-M3S7-M3S8-M3S9-P1S1-P1S10-P1S11-P1S12-P1S13-P1S14-P1S15-P1S16-P1S17-P1S18-P1S19	37.466076	0.015000
7	Otu007	P2S2-P2S20-P2S21-P2S22-P2S23-P2S24-P2S25-P2S26-P2S27-P2S28-P2S29-P2S3-P2S4-P2S5-P2S6-P2S7-P2S8-P2S9-P3S1-P3S10	41.481815	0.016000
7	Otu010	M3S12-M3S2-M3S3-M3S4-M3S5-M3S6-M3S7-M3S8-M3S9-P1S1-P1S10-P1S11-P1S12-P1S13-P1S14-P1S15-P1S16-P1S17-P1S18-P1S19	47.395081	0.007000
7	Otu011	M3S12-M3S2-M3S3-M3S4-M3S5-M3S6-M3S7-M3S8-M3S9-P1S1-P1S10-P1S11-P1S12-P1S13-P1S14-P1S15-P1S16-P1S17-P1S18-P1S19	44.400589	0.011000
7	Otu013	P1S2-P1S20-P1S3-P1S4-P1S5-P1S6-P1S7-P1S8-P1S9-P2S1-P2S10-P2S11-P2S12-P2S13-P2S14-P2S15-P2S16-P2S17-P2S18-P2S19	49.684628	0.006000
7	Otu014	M3S12-M3S2-M3S3-M3S4-M3S5-M3S6-M3S7-M3S8-M3S9-P1S1-P1S10-P1S11-P1S12-P1S13-P1S14-P1S15-P1S16-P1S17-P1S18-P1S19	28.282827	0.028000
7	Otu016	M3S12-M3S2-M3S3-M3S4-M3S5-M3S6-M3S7-M3S8-M3S9-P1S1-P1S10-P1S11-P1S12-P1S13-P1S14-P1S15-P1S16-P1S17-P1S18-P1S19	29.833334	0.046000
7	Otu026	M3S12-M3S2-M3S3-M3S4-M3S5-M3S6-M3S7-M3S8-M3S9-P1S1-P1S10-P1S11-P1S12-P1S13-P1S14-P1S15-P1S16-P1S17-P1S18-P1S19	29.753695	0.018000
7	Otu028	M3S12-M3S2-M3S3-M3S4-M3S5-M3S6-M3S7-M3S8-M3S9-P1S1-P1S10-P1S11-P1S12-P1S13-P1S14-P1S15-P1S16-P1S17-P1S18-P1S19	46.837257	0.005000
...

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

mothur > indicator(shared=stool.final.an.shared, design=stool.design)
Species	Indicator_Groups	IndicatorValue	pValue
Otu0001	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	93.725014	0.002000
Otu0003	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	90.909096	<0.001000
Otu0004	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	64.701805	0.030000
Otu0009	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	63.636364	0.015000
Otu0011	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	68.012146	0.043000
Otu0012	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	82.823242	0.010000
Otu0013	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	64.501587	0.029000
Otu0015	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	54.545456	0.027000
Otu0022	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	54.545456	0.031000
Otu0028	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	66.666672	0.013000
Otu0033	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	95.897446	<0.001000
Otu0043	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	63.636364	0.017000
Otu0045	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	70.710602	0.036000
Otu0046	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	81.007751	0.003000
Otu0065	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	66.666672	0.010000
Otu0067	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	61.002953	0.039000
Otu0082	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	56.619896	0.045000
Otu0090	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	66.666672	0.013000
Otu0096	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	70.734909	0.036000
Otu0099	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	79.519569	0.006000
Otu0108	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	91.666672	<0.001000
Otu0114	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	53.501976	0.044000
Otu0126	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	60.707493	0.022000
Otu0127	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	67.988068	0.028000
Otu0135	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	58.333332	0.026000
Otu0142	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	54.815739	0.035000
Otu0146	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	60.642685	0.043000
Otu0148	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	63.636364	0.021000
Otu0197	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	67.274681	0.021000
Otu0201	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	50.000000	0.036000
Otu0227	F11Fcsw-F12Fcsw-F13Fcsw-F14Fcsw-F21Fcsw-F22Fcsw-F24Fcsw-F31Fcsw-F32Fcsw-F33Fcsw-F34Fcsw	63.636364	0.016000
Otu0290	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	58.333332	0.015000
Otu0308	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	56.410252	0.038000
Otu0332	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	59.459461	0.024000
Otu0409	M11Fcsw-M12Fcsw-M13Fcsw-M14Fcsw-M21Fcsw-M22Fcsw-M23Fcsw-M24Fcsw-M41Fcsw-M42Fcsw-M43Fcsw-M44Fcsw	50.000000	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)

Revisions

  • 1.29.0 Added group info to indicator results.
  • 1.31.0 Added multiple processors for Windows.
  • 1.31.0 Bug Fix: problem with pvalues when multiple processors were used.
  • 1.40.0 Speed and memory improvements for shared files. #357 , #347
  • 1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.