Man pages for eclarke/sarcoid-microbiome-paper
Figures for the Clarke et al sarcoid microbiome paper
| cairo_failsafe | Try to use 'cairo_pdf', but fall back to 'pdf' if that... |
| counts_matrix | Creates a counts matrix from an agglomerated data frame.... |
| ExtractSignificantResults | Extracts the significant results from... |
| fct_anon_deterministic | Non-random version of 'forcats::fct_anon' |
| LinkMatchedControls | Links matched samples and (environmental) controls via the... |
| load_data | Load datasets. |
| LoadData | Load datasets (memoized). |
| MakeBarchartData | Groups taxa into top members and samples by their larger... |
| MakeHeatmapData | Prepare agglomerated dataframe for heatmap display by... |
| MakePCOAData | Performs principle coordinates analysis on a GUniFrac... |
| MakeTopBarchartData | Prepares data for making the summary barcharts showing the... |
| MakeUnifracData | Calculates the generalized UniFrac distances for an... |
| min_rank | Creates a MinRank vector from an agglomerated data frame... |
| PCoAChunk | Wrapper for UniFrac calculations, PERMANOVA testing and PCoA... |
| PlotBarchart | Plots the results of MakeBarchartData as a set of grouped... |
| PlotHeatmap | Plot the results of MakeHeatmapData. |
| PlotPCOA | Standardized PCoA plot. |
| PlotTopBarcharts | Plots data prepared by MakeTopBarchartData. |
| root_tree | Root a tree using a random node as the root. |
| RunDESeq2 | Test differences between study groups using DESeq2. |
| RunGLMM | Test differences between study groups using the generalized... |
| StandardizeMetadata | Standardize a metadata table (s) to be compatible with... |
| TestMatchedControlMixedModel | Create and test a mixed effect model between two sample types... |
| TestPermanova | Performs PERMANOVA on the given terms using the unifrac... |
