How to use maaslin_plot_results_from_output(

Downstream analysis and statistics MaAsLin
1

Hi,
I’m not very familiar with this function, I mean I want to show a particular species.Not working at present

maaslin_plot_results_from_output('output',
                                 metadata1,
                                 'TSS',
                                 'LOG',
                                 feature_specific_covariate_name = c('Bacteroides_uniformis',
                                                                'Roseburia_inulinivorans',
                                                                'Lachnospira_pectinoschiza'),
                                 feature_specific_covariate_record = NULL,
                                 median_comparison_abundance = TRUE,
                                 median_comparison_prevalence = FALSE,
                                 max_significance = 0.1,
                                 plot_summary_plot = TRUE,
                                 summary_plot_first_n = 25,
                                 coef_plot_vars = NULL,
                                 heatmap_vars = NULL,
                                 plot_associations = TRUE,
                                 max_pngs = 30,
                                 balanced = FALSE,
                                 save_plots_rds = FALSE)

Best,
JianXiZhang

2

Hi JianXiZhang,

Sorry for the confusion - that’s not how the function works. The parameter feature_specific_covariate_name is for use with the feature_specific_covariate when there’s a feature-specific covariate to control for (e.g., DNA abundance in a metatranscriptomics experiment).

The plotting function isn’t designed to show particular features, but you could improvise with either of the following options. First, if you just subset your results tables to the taxa you care about, only those will be plotted. Second you could copy the plotting functions here and manually set signif_taxa to force them to be plotted.

Will

3

I used the second method, which is currently solved.
Thanks