make_distance_comparison_plots error:I want to compare the same group.

[iyomi...@gmail.com]

Dear QIIME user

I run "make_distance_comparison_plots" comparing A（disease mouse） & B(control mouse)  groups in SampleType category.(I compared A-B.)

make_distance_comparison_plots.py -m map.txt -d beta/unweighted_unifrac_dm.txt -f SampleType -c 'disease_mouse' -o comparison_output/ --x_tick_labels_orientation horizontal


Now I want to compare the distance among A(disease mouse) group.(I want to compare A-A)
Is it possible to run ?

Thank you for your kindness help !

Beat Regards
Iyo

[iyomi...@gmail.com]

Additional..

It is first time to use forum for me.

And I made mistake topic name,I understand it's not error.But I don't know how to correct topic name.I'm soory.

How to run make_distance_comparison_plots.py for among one group.

I want to know command for it.

I want to make bar chart among one group.But I can't.

Please show me.

Best
Iyo

[abir...@gmail.com]

Hi, Iyo,

Welcome to the forum!  If you want to make a box plot showing the spread of values for a particular measurement for  all samples within a single group, try the alternate script "make_distance_boxplots" (instead of "make_distance_comparison_plots")--see the description at http://qiime.org/scripts/make_distance_boxplots.html : "The boxplots that are created compare distances within all samples of a field value, as well as between different field values".

Best,

Amanda

[iyomi...@gmail.com]

Dear Amanda

Thank you for your massage.

Thank you give me a tip of box plots.


Actually,I want to make the figure like Fig2(b)&(d) on this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4569432/　.
At Fig2(b)&(d),author compared HC-HC(control-control),HC-MS(control-disease group),MS-MS(disease group-disease group) using bar chart.


Now I'm using map.txt,showing below.

#SampleID    BarcodeSequence    LinkerPrimerSequence    SampleType    Description
M1    ATCACCAGGTGT    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M2    TCCCTTGTCTCC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M3    ATCCTTTGGTTC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M4    AACCTTTGGTTC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M5    AAAATTTGGTTC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M6    ATTAAATGGTTC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M7    AAAAATTGGTTC    CAAGCAGAAGACGGCATACGAGAT    control_mouse    mouse feces
M8    AAAAAAAGGTTC    CAAGCAGAAGACGGCATACGAGAT    control_mouse    mouse feces
M9    AAAAAAAAGTTC    CAAGCAGAAGACGGCATACGAGAT        control_mouse    mouse feces
M10    AGGGGGGGGGAC    CAAGCAGAAGACGGCATACGAGAT    control_mouse    mouse feces
M11    AAGGTTACAAAC    CAAGCAGAAGACGGCATACGAGAT    control_mouse    mouse feces
M12    ATTAAATGGTTG    CAAGCAGAAGACGGCATACGAGAT    control_mouse    mouse feces


And I run "make_distance_comparison_plots" comparing  disease mouse(A) & control mouse(B)  groups in SampleType category.
But I can't make bar cart comparing A-A,B-B.

I tried making map.txt below for coparing A-A.

M1    ATCACCAGGTGT    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M1    ATCACCAGGTGT    CAAGCAGAAGACGGCATACGAGAT    mouse                 mouse feces
M2    TCCCTTGTCTCC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M2    TCCCTTGTCTCC    CAAGCAGAAGACGGCATACGAGAT    mouse                  mouse feces
M3    ATCCTTTGGTTC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M3    ATCCTTTGGTTC    CAAGCAGAAGACGGCATACGAGAT    mouse                  mouse feces
M4    AACCTTTGGTTC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M4    AACCTTTGGTTC    CAAGCAGAAGACGGCATACGAGAT    mouse                 mouse feces
M5    AAAATTTGGTTC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M5    AAAATTTGGTTC    CAAGCAGAAGACGGCATACGAGAT    mouse                 mouse feces
M6    ATTAAATGGTTC    CAAGCAGAAGACGGCATACGAGAT    disease_mouse    mouse feces
M6    ATTAAATGGTTC    CAAGCAGAAGACGGCATACGAGAT    mouse                 mouse feces

It run. But I don't know this way is really right?
Every time making map.txt for analysis is little bit strange.I can't get the bar cart all 3 bars together is the big problem.
Becase I run each A-A,A-B,B-B. But I want to get the all A-A,A-B,B-B bars at one time.

How should  I do?

Best Regars
Iyo

[abir...@gmail.com]

Hi, Iyo,

Thank you for providing an example of what you're looking for from a paper.  As far as I know, there is no functionality in QIIME that will do precisely what you want here; however, you could create such a chart yourself (using Excel, or R, or python) by calculating the required means and standard deviations from the relevant entries in your distance matrix file.

Best,

Amanda

[iyomi...@gmail.com]

Dear Amanda

Thank you for your message.I understand.I'll challenge to lean making figure by other way.
I feel very lucky meeting kindness person like you at the first time using forum.
Thank you so much!

Best Regards
Iyo