View source: R/taxa_by_sample_type_functions.R
taxa_summary_by_sample_type | R Documentation |
Function to show contributions of specific taxa to variation among communities using Mann-Whitney (2 factor levels), Kruskal-Wallis (more than 2) tests, or more complex models.
taxa_summary_by_sample_type( taxa_smry_df, metadata_map, type_header, filter_level, test_type, grouping_factor, custom_test_function, smry_fun = mean, out_fp )
taxa_smry_df |
Taxa summary data frame. |
metadata_map |
The metadata mapping data frame. |
type_header |
Mapping file header (in quotation marks) of factor for which you are testing for differences. |
filter_level |
[OPTIONAL] The minimum mean value needed in at least one. of the factor levels for a taxon to be retained in the analysis. |
test_type |
[OPTIONAL]. If omitted, no test is performed and no p-values are reported. Otherwise, either 'MW', 'KW', or 'custom' (i.e. Wilcoxon/Mann-Whitney U for 2 factor levels or Kruskal-Wallis for more than two factor levels). See details for custom test/model implementation. |
grouping_factor |
[OPTIONAL] Used with 2-way tests. |
custom_test_function |
[OPTIONAL] Name of custom test function. |
smry_fun |
[OPTIONAL] The function to summarize values by (Default: mean). |
out_fp |
[OPTIONAL] Test results output filepath. Written as a csv file. |
ts = summarize_taxonomy(fruits_veggies, level = 2) # differences in relative abundances of phyla across fruits/veggies taxa_summary_by_sample_type( ts, metadata_map = fruits_veggies$map_loaded, type_header = 'Sample_type', filter_level = 0.03, test_type = 'KW' ) # differences in relative abundances of phyla between farm types taxa_summary_by_sample_type( ts, metadata_map = fruits_veggies$map_loaded, type_header = 'Farm_type', filter_level = 0.03, test_type = '2WNP', grouping_factor = 'Sample_type' )
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