Man pages for TBrach/MicrobiomeX
eXtended Functions for Microbiome Analysis and Visualization

biplot_bcaDraw a between class analysis (BCA) plot.
biplot_pcoaDraw a principal coordinate biplot using Bray-Curtis...
boxplot_taxonMake boxplot of taxon abundance stratified by one sample...
distance_t_analyseWithin- and between-group beta-diversity analysis
draw_taxa_heatmapDraw a heatmap of the OTU abundances in a phyloseq object.
filter_resultsFilter differential test results for specific taxa
format_hitsFormat differential test results to be presentable
format_hits_for_heatmapFormat significant hits results so that it can be shown as an...
get_my_palette_colorsGet palette color maps for a variable from a custom palette...
get_my_palette_nameGet the name of the custom palette for a given variable
get_permanova_tableMake knitr table from Permanova results
get_pretty_taxon_nameGet presentable name for a taxon
get_significance_stringGet statistical significance level strings for P-values.
get_taxon_by_idGet taxonomy annotation for a given id in a phyloseq object
gm_ownCalculate geometric mean of a vector.
helloHello, World!
knit_hits_tableMake knitr table of differential results
make_heat_map_from_physeqInternal function to draw heatmap from a physeq object.
plot_pcoaDraw a principal coordinate plot using Bray-Curtis...
run_contrast_2_levelsExtract DESeq2 results
tabulate_factorsTabulate interaction between two factors in the sample_data...
test_differential_abundance_DESeq2DESeq2 - negative binomial Wald test
test_differential_abundance_KruskalKruskal-Wallis differential abundance test
test_differential_abundance_WilcoxonWilcoxon rank sum differential abundance test
test_differential_prevalenceDifferential prevalence testing
TBrach/MicrobiomeX documentation built on May 14, 2019, 2:28 p.m.