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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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I count not arrange my sample from same group together #1679

Open Hina1112 opened 1 year ago

Hina1112 commented 1 year ago

I am making a graph plot from out table, when the result came my samples from same group go far apart from each other. LF1,LF2,LF3 and HF1, HF2, HF3.. I want them to be like LF1,LF2.. hf1, hf2, hf3 but it comes out like HF1, LF2, HF2, LF3, LF2, HF3

Hina1112 commented 1 year ago

I am making graph in R studio.

Hina1112 commented 1 year ago

OTU table***

RachBioHaz commented 11 months ago

I am making a graph plot from out table, when the result came my samples from same group go far apart from each other. LF1,LF2,LF3 and HF1, HF2, HF3.. I want them to be like LF1,LF2.. hf1, hf2, hf3 but it comes out like HF1, LF2, HF2, LF3, LF2, HF3

Not sure if this is related to a specific bug you're experiencing or just want some advice. If it's a bug, can you provide the code you are using to create the plot? It will help identify the functionality issue.

If it's just advice, are you using a specific factor to group by? It might be grouping them together on some other basis if a factor has not been set or selected.

Factor info here: https://github.com/joey711/phyloseq/issues/209

Plot info here: https://github.com/joey711/phyloseq/issues/1676

Some suggestions to try: 1) You can set and change factors in the phyloseq object if you just want samples grouped together based on a specific factor, e.g treatment group.

A) Check if the factor has already been set levels(sample_data(pc)$column_name)

B) Set the factor in the order needed sample_data(ps)$column_name <- factor( sample_data(ps)$column_name, levels = c( "1st-Factor", "2nd-Factor", ... "last-factor"))

C) Change the factor name if needed
sample_data(ps)$column_name <- factor( sample_data(ps)$column_name, labels = c( "1-F", "2-F", ... "L-F"))

2) If you want to specify the exact order of samples to output, try the package below to list the specific order of the samples: https://david-barnett.github.io/microViz/reference/ps_reorder.html

hope this helps