Distruct: graph of individual Q-matrix
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Viola Grugni
Nov 21, 2012, 9:04:35 AM11/21/12
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Hello everybody,
I am using Distruct for the first time and I have problems with the
graph of individual Q-matrix.
This is my .popq file.
1: 0.132 0.135 0.415 0.118 0.199 2478
2: 0.490 0.084 0.125 0.037 0.264 587
3: 0.323 0.136 0.102 0.030 0.410 1035
4: 0.314 0.009 0.108 0.286 0.283 905
5: 0.228 0.035 0.240 0.133 0.365 826
6: 0.091 0.574 0.260 0.036 0.039 274
7: 0.320 0.230 0.145 0.027 0.278 726
If I set PRINT_INDIVS to 0 everything goes well and I obtain the
graph. If I set PRINT_INDIVS to 1 I obtain an error (the population to
which individual 1 belongs 1296624 is not listed in file .popq.)
These are the first lines of my .indivq file.
1 1 (0) 1 : 0.941 0.034 0.004 0.016 0.005
2 2 (0) 1 : 0.946 0.035 0.007 0.007 0.005
3 3 (0) 1 : 0.938 0.039 0.008 0.011 0.004
4 4 (0) 1 : 0.954 0.028 0.005 0.010 0.004
5 5 (0) 1 : 0.947 0.033 0.008 0.009 0.004
6 6 (0) 1 : 0.017 0.953 0.012 0.014 0.004
7 7 (0) 1 : 0.019 0.956 0.010 0.010 0.005
8 8 (0) 1 : 0.012 0.973 0.005 0.005 0.005
9 9 (0) 1 : 0.014 0.967 0.006 0.009 0.005
10 10 (0) 1 : 0.017 0.967 0.005 0.007 0.004
This was the original file taken from Structure output.
1 ht2 (0) 1 : 0.941 0.034 0.004 0.016 0.005
2 ht2_2 (0) 1 : 0.946 0.035 0.007 0.007 0.005
3 ht2_3 (0) 1 : 0.938 0.039 0.008 0.011 0.004
4 ht3 (0) 1 : 0.954 0.028 0.005 0.010 0.004
5 ht3_2 (0) 1 : 0.947 0.033 0.008 0.009 0.004
6 ht4 (0) 1 : 0.017 0.953 0.012 0.014 0.004
7 ht4_2 (0) 1 : 0.019 0.956 0.010 0.010 0.005
8 ht8 (0) 1 : 0.012 0.973 0.005 0.005 0.005
9 ht8_2 (0) 1 : 0.014 0.967 0.006 0.009 0.005
10 ht8_3 (0) 1 : 0.017 0.967 0.005 0.007 0.004
What could be the error inside this file? I tried to reproduce all the
spaces and punctuation of casia.indivq but the problem persist.
Thank you!!
Viola
I am using Distruct for the first time and I have problems with the
graph of individual Q-matrix.
This is my .popq file.
1: 0.132 0.135 0.415 0.118 0.199 2478
2: 0.490 0.084 0.125 0.037 0.264 587
3: 0.323 0.136 0.102 0.030 0.410 1035
4: 0.314 0.009 0.108 0.286 0.283 905
5: 0.228 0.035 0.240 0.133 0.365 826
6: 0.091 0.574 0.260 0.036 0.039 274
7: 0.320 0.230 0.145 0.027 0.278 726
If I set PRINT_INDIVS to 0 everything goes well and I obtain the
graph. If I set PRINT_INDIVS to 1 I obtain an error (the population to
which individual 1 belongs 1296624 is not listed in file .popq.)
These are the first lines of my .indivq file.
1 1 (0) 1 : 0.941 0.034 0.004 0.016 0.005
2 2 (0) 1 : 0.946 0.035 0.007 0.007 0.005
3 3 (0) 1 : 0.938 0.039 0.008 0.011 0.004
4 4 (0) 1 : 0.954 0.028 0.005 0.010 0.004
5 5 (0) 1 : 0.947 0.033 0.008 0.009 0.004
6 6 (0) 1 : 0.017 0.953 0.012 0.014 0.004
7 7 (0) 1 : 0.019 0.956 0.010 0.010 0.005
8 8 (0) 1 : 0.012 0.973 0.005 0.005 0.005
9 9 (0) 1 : 0.014 0.967 0.006 0.009 0.005
10 10 (0) 1 : 0.017 0.967 0.005 0.007 0.004
This was the original file taken from Structure output.
1 ht2 (0) 1 : 0.941 0.034 0.004 0.016 0.005
2 ht2_2 (0) 1 : 0.946 0.035 0.007 0.007 0.005
3 ht2_3 (0) 1 : 0.938 0.039 0.008 0.011 0.004
4 ht3 (0) 1 : 0.954 0.028 0.005 0.010 0.004
5 ht3_2 (0) 1 : 0.947 0.033 0.008 0.009 0.004
6 ht4 (0) 1 : 0.017 0.953 0.012 0.014 0.004
7 ht4_2 (0) 1 : 0.019 0.956 0.010 0.010 0.005
8 ht8 (0) 1 : 0.012 0.973 0.005 0.005 0.005
9 ht8_2 (0) 1 : 0.014 0.967 0.006 0.009 0.005
10 ht8_3 (0) 1 : 0.017 0.967 0.005 0.007 0.004
What could be the error inside this file? I tried to reproduce all the
spaces and punctuation of casia.indivq but the problem persist.
Thank you!!
Viola
Vikram Chhatre
Nov 21, 2012, 9:22:35 AM11/21/12
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What are the ht designations? Did you obtain the pre-clumpp files
from Harvester or manually? If you want, send me all the files off
the list and I will try it out here.
---------------------------------------
Vikram Chhatre
Graduate Program in Genetics
Texas A&M University
cryptic...@gmail.com
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from Harvester or manually? If you want, send me all the files off
the list and I will try it out here.
---------------------------------------
Vikram Chhatre
Graduate Program in Genetics
Texas A&M University
cryptic...@gmail.com
This message was sent from a cellular device. It may contain typos and
other errors.
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Viola
Dec 12, 2012, 4:56:55 AM12/12/12
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Hi,
thanks to Vikram I solved the problem.
I used Structure Harvester to obtain the correct input file. Furthermore, I discovered that Distruct does not work with more than 5000 individuals.
Viola
thanks to Vikram I solved the problem.
I used Structure Harvester to obtain the correct input file. Furthermore, I discovered that Distruct does not work with more than 5000 individuals.
Viola
Anique GBOTTO
Dec 13, 2012, 6:40:00 AM12/13/12
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Hi,
Thank you for your help Viola
and many thanks to Vikram
I opened the file .ps with ghostview. I get just one graph with population information. Is there something special to do to have graph with individuals. Furthermore, I would like to have a graph in which populations are grouped by cluster. Could you please help me?
Best wishes!!!
Thank you for your help Viola
and many thanks to Vikram
I opened the file .ps with ghostview. I get just one graph with population information. Is there something special to do to have graph with individuals. Furthermore, I would like to have a graph in which populations are grouped by cluster. Could you please help me?
Best wishes!!!
2012/12/12 Viola <viola....@gmail.com>
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Viola
Dec 13, 2012, 7:32:07 AM12/13/12
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I'm glad I could help.
To obtain a graph with individuals you have to put PRINT_INDIVS equal to 1 and the program will automatically cluster them in populations.
Best,
Viola
To obtain a graph with individuals you have to put PRINT_INDIVS equal to 1 and the program will automatically cluster them in populations.
Best,
Viola
2012/12/12 Viola <viola....@gmail.com>
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Anique GBOTTO
Dec 13, 2012, 8:02:07 AM12/13/12
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This is what I did, but it does not work. Furthermore, I would like to have a graph in which populations are grouped by cluster. Could you please help me?
Yours sincerely
Niquie
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Functional Genomics and Genetic improvement laboratory
Yours sincerely
Niquie
2012/12/13 Viola <viola....@gmail.com>
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AHOU ANIQUE GBOTTO
Natural Sciences, Ph.D student
Biodiversity and Ecosystem management
Genetic and molecular biology
02 BP 801 Abidjan 02 (University of d'Abobo Adjamé, Côte d'Ivoire)
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Building a future in which humans live
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For a living planete; WWFViola
Dec 13, 2012, 8:30:55 AM12/13/12
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Did you obtain the file for individuals from CLUMPP?
2012/12/13 Viola <viola....@gmail.com>
2012/12/12 Viola <viola....@gmail.com>
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Functional Genomics and Genetic improvement laboratoryAHOU ANIQUE GBOTTONatural Sciences, Ph.D studentBiodiversity and Ecosystem managementGenetic and molecular biology
02 BP 801 Abidjan 02 (University of d'Abobo Adjamé, Côte d'Ivoire)Phone: (225) 23 46 26 12Fax. (225) 20 30 43 00GSM. (225) 57 97 24 14/ (225) 40 65 33 46
Anique GBOTTO
Dec 13, 2012, 8:34:24 AM12/13/12
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yes
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2012/12/13 Viola <viola....@gmail.com>
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AHOU ANIQUE GBOTTO
Natural Sciences, Ph.D student
Biodiversity and Ecosystem management
Genetic and molecular biology
02 BP 801 Abidjan 02 (University of d'Abobo Adjamé, Côte d'Ivoire)
Phone: (225) 23 46 26 12
Fax. (225) 20 30 43 00
GSM. (225) 57 97 24 14/ (225) 40 65 33 46
Vikram Chhatre
Dec 13, 2012, 8:37:20 AM12/13/12
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Niquie -
Can you post the graph you have and the parameter file?
---------------------------------------
Vikram Chhatre
Graduate Program in Genetics
Texas A&M University
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Anique GBOTTO
Dec 13, 2012, 8:56:59 AM12/13/12
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Vikram,
Find enclosed all. But I can't save the graph. when I try to save it with pdf creator, I get this (see lana.pdf).
Yours
Find enclosed all. But I can't save the graph. when I try to save it with pdf creator, I get this (see lana.pdf).
Yours
2012/12/13 Vikram Chhatre <cryptic...@gmail.com>
Vikram Chhatre
Dec 13, 2012, 10:57:10 AM12/13/12
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Niquie,
Please see the attached archive. I only made aesthetic changes to your drawparameters file. Check the PDF to see if thats what you wanted. Then you can compare your original drawparams with the one in this archive.
If this is still not what you wanted, you may wish to provide an example figure.
V
Anique GBOTTO
Dec 14, 2012, 5:45:44 AM12/14/12
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Hi Vikram,
Thank you for your help
I want something like on the figure below. On which, population are grouped by cluster.
Thanks!
Niquie
2012/12/13 Vikram Chhatre <cryptic...@gmail.com>
Anique GBOTTO
Dec 15, 2012, 5:45:42 AM12/15/12
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Hello Vikram
Do you think that there is a solution for my request?
Best regards,
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Vikram Chhatre
Dec 15, 2012, 9:13:11 AM12/15/12
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Niquie,
In the figure that you attached, different colors represent individual clusters and every population has at least some membership in more than one cluster. Thats exactly how Distruct makes the graph. Am I missing something here? I think Distruct is doing what you need.
V
Julie Hebert
Dec 15, 2012, 11:47:41 AM12/15/12
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Niquie,
I'm going to hazard a guess that what is missing is the labels you want. My suggestion is one of two things: either take the original distruct output (sorted by each K in some decreasing order) and add the labels manually in another program. Or, you can sort your indivq file by the population membership, then change the populations to meet your requirements (e.g., A becomes pop1, B becomes pop2, etc.) then set up your labels that way. You'll need to reconfigure your popq file, but you can do that by averaging the K values in each column for each population. It does what is needed for distruct. Finally, I don't know that you can make distruct output the two line label for popB, but you could break up popB into two pops, one for each species, then label each of those. Let me know if that doesn't make sense.
Julie
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Anique GBOTTO
Dec 15, 2012, 1:15:59 PM12/15/12
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Vikram,
Thank you. You are right.
Thank you. You are right.
But I think Julie suggestions will help. I will try and tell you!
Yours sincerely,
Niquie
2012/12/15 Vikram Chhatre <cryptic...@gmail.com>
Anique GBOTTO
Dec 16, 2012, 6:50:25 AM12/16/12
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Hi Vikram,
-
I tried to run DISTRUT with few modifications to the files .languages and .names. Before, I grouped populations according to K to which they belong and sorted by each K in some decreasing order. The graph I obtained is not different from the source one.
Many thanks for giving me your assistance,
You were a great help for me!
Yours sincerely!
Niquie
2012/12/15 Anique GBOTTO <niqui...@gmail.com>
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