Question: Sorting taxonomy table
gravatar for arsilan324
13 months ago by
arsilan32480 wrote:

Hi all,

I am trying to sort OTU table with assigned taxonomy; it looks like this (only four rows are shown below),

Treatment_A Value_A Treatment_B Value_B Treatment_C Value_C

Sulfuritalea    1492    Sulfuritalea    1273    Sulfuritalea    3770    Sideroxydans    6480
Sulfuritalea    683 Sulfuritalea    526 Sulfuritalea    1898    Sulfuritalea    2302
Dechloromonas   150 Dechloromonas   153 Methylosarcina  525 Sulfuricurvum   1224
Staphylococcus  131 Methylosarcina  103 Sideroxydans    435 Sideroxydans    1078

Now, what I want to do is

  1. I want to add absolute numbers of all similar taxon given in same column to single value (row).
  2. Arrange all similar taxon of different treatments in front of each other so that I can make boxplot for comparison.

Can anyone suggest me how to do that? Maybe this is a very basic thing to do in R, but I am not really bioinformatics person. I am a PhD student doing molecular biology and so don't know much about this stuff. I would really appreciate help on this matter.

Best regards Arslan

next-gen R otu_table • 281 views
ADD COMMENTlink written 13 months ago by arsilan32480

Is your data correct? If I am understanding it correctly, treatments A, B and C have two values for Sulfuritalea, which seems wrong to me.

ADD REPLYlink written 13 months ago by h.mon29k

Yes, it has multiple values of same taxon in each column. So first of all i want to combine (sum) them to make a single value and then arrange them.

ADD REPLYlink written 13 months ago by arsilan32480
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