Add sample names to Abundance Plot

[microbiome]

Add sample names to Abundance Plot

[FelixErnst]

Should the issue be closed?

[antagomir]

You can do: plotAbundance(se, add_x_text=TRUE)

I have now added an example on function manpage in a forthcoming PR.

See help("mia-plot-args") for more options (mentioned in function manpage but yep, perhaps a bit difficult to find).

[asierFernandezP]

Thank you! But is it also possible to display the group names (of the grouping variable that it is used in order_sample_by) instead of the individual sample names? Otherwise it is difficult to fit all the individual names in the plot.

[antagomir]

Do you something like

plotAbundance(se, features = "SampleType")

[asierFernandezP]

Yes, but this does indeed generate another barplot for the groups, right? And I could then merge both together using wrap_plots. But I was trying to add only the group names (once for all the samples belonging to the same group) to the X axis of the abundance plots (as samples have already been ordered by groups) or add something that indicates the different groups of the samples without the need of adding this additional plot generated by features = "SampleType".

[antagomir]

Right. I am not sure if this is easily possible currently. It is rather complicated scenario to have in a general case, where the group sizes and numbers of groups can potentially vary a lot. Also not sure how good ggplot support there is to this feature. Ideally, this could utilize already existing ggplot techniques. If there are pointers, we could have a look.

[asierFernandezP]

Yes, thank you very much! I guess this is a rather specific case.

[FelixErnst]

Can you provide a workable example descibing your case?

I think the easiest solution would be to create a temporary object and rename the colnames. SOmething like this;

tmp <- se
colnames(tmp) <- colData(tmp)$whatever
plotAbundance(se, add_x_text=TRUE)

Depending on your number of samples, this might look ok, but I would try to optimize the wrapping of the two objects. The example give in https://microbiome.github.io/miaViz/reference/plotAbundance.html

Can be tweaked using the patchwork functions. For example you can remove labels from the second object and print it 1/10th of hight of the first object. FOr more details have a look here https://patchwork.data-imaginist.com/