Hello, i am working with a set of microbiome data from livestock. I have used maaslin3 to look for taxa associated with my experimental variable (for this post referred to as ‘red’ apologies, this data is still unpublished). i used the following formula
~red + green (1|blue)
maaslin ran as intended and in the output i can see a summary plot and association plots for my ‘red’ variable. in the significant_results.tsv i can see the following
(here the red rows indicate taxa with red positive). I can see i have significant results, however when i try and remake the summary plot to only include my experimental variable, only the association plots are available, i do not get a summary plot.
sig_plot_data<-maaslin3::maaslin_plot_results_from_output(
output = “mas3.output”,
metadata = maslin.meta_data.s,
normalization = “TSS”,
transform = “LOG”,
summary_plot_first_n = 20,
coef_plot_vars = c(“RedPositive”,“RedNegative”),
heatmap_vars = c(“RedPositive”,“RedNegative”),
plot_summary_plot = TRUE
)
sig_plot_data$ only association plots not summary
apologies if this is clearly a rookie error but any help is really appreciated!
kindest regards
Will