Tools for visualization of taxonomic/gene/COG abundance in samples

Question

[allerdrengen55]

Hi!

I'm looking for tools that can help me visualize my data. I have 4 samples, in the same format. And I'm looking for a smart method of visualizing the comparison of the 4 samples in the same bar/plot/chart. I have tried with Phylophlan and Krona , but Phylophlan seemed a bit overkill (also hard to use) and I couldn't get Krona to properly compare my data (and it looked weird). Any bar/plot/chart tools are appreciated.

My data is basically a table of abundances in a tab-separated file like (each file is probably 20-25 lines long):

abundance(of genes)    taxonomy    cogs    genes

If a tool takes a different input, I would have no problem in altering the format of my data.

[Mark]

Can you expand on what you want to visual/convey? For example do you want to compare the COG distribution or taxonomy? I think ggplot2 in R would be the most applicationa and easiest to use. Post a snippet of the data and someone can give you a better idea.

[allerdrengen55]

So there are basically two things Id like to compare between the samples:

1. Taxonomies. So the abundance of different bacteria in my samples. In the format:

 34 Lactobacillus
 93 E.Coli

etc. I was thinking some sort of circle chart (like phylophlan).

2 Abundance of different COGs between the samples:

43 Amino acid transport and metabolism

94 Signal transduction mechanisms

The two sets can be compared differently, but would also be cool to compare them together somehow (COGs in different taxonomic groups)

[Mark]

ggplot2 for sure. You're after custom plots that no bioinfo software will produce for you. It might be a bit of a slog at the start but its well worth it to learn R/ggplot2.

[allerdrengen55]

Thanks, I'll look into it!