indicator
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. Default processors=Autodetect number of available processors and use all available.
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.
- 1.45.0 Fixes bug with indicator command pvalues. #729