Man pages for schuyler-smith/phylosmith
Functions to help analyze data as phyloseq objects
| abundance_heatmap | Create a heatmap of the out_table from a phyloseq-object. |
| abundance_lines | Create a lineplot ggplot object of the abundance table from a... |
| alpha_diversity_graph | Create a boxplot of the alpha-diversity. Function from the... |
| arrange_co_occurrence_table | Arrange co-occurence table |
| assign_rank | Assign rank values to a matrix. |
| bin | Bin data |
| change_labels | Change names of factors in graph_data to change labels in... |
| check_index_classification | Converts numeric values to column names in tax_table |
| check_index_treatment | Converts numeric values to column names in sample_data. |
| check_TaR | phyloseq object so taxa are rows. |
| CI_ellipse | Creates confidence interval ellipse for scatterplot |
| common_taxa | Find taxa shared between treatments of a phyloseq object.... |
| conglomerate_samples | Merge samples based on common factor within sample_data. |
| conglomerate_taxa | Conglomerate taxa by sample on a given classification level.... |
| co_occurrence | Pair-wise Spearman rank co-occurrence. |
| co_occurrence_network | Create a node network ggplot object of the co-occurrence from... |
| Correlation | Co-occurrence calculation |
| create_palette | Creates color palettes for figures. |
| curate_co_occurrence | Curate co-occurrence data. Function from the... |
| dendrogram_phyloseq | Create a ggplot object of the dendrogram from a phyloseq... |
| histogram_permuted_rhos | Create a ggplot object of the distribution of rho values from... |
| ia_lakes | IA Lake Data |
| library_size | Normalizes abundance data in an 'otu_table' using library... |
| melt_phyloseq | Melt a phyloseq object into a data.table. Function from the... |
| merge_treatments | Combine meta-data columns. Function from the... |
| mock_phyloseq | Mock Phyloseq Object 1 |
| mock_phyloseq_2 | Mock Phyloseq Object 2 |
| network_layout_ps | Create an layout_igraph object of the co-occurrence from a... |
| network_ps | Create an igraph network object of the co-occurrence from a... |
| nmds_phyloseq | Create a ggplot object of the NMDS from a phyloseq object.... |
| pcoa_phyloseq | Create a ggplot object of the PCoA from a phyloseq object.... |
| permute_rho | Permutes the pair-wise Spearman rank co-occurrence, to... |
| permute_rho_Rcpp | Co-occurrence rho calculations |
| phylogeny_profile | Create a ggplot object of the phylogenic barplots from a... |
| phylosmith | phylosmith-package |
| quantile_permuted_rhos | Calculate quantiles for the permuted rho values from the... |
| relative_abundance | Transform abundance data in an 'otu_table' to relative... |
| set_sample_order | Re-orders the samples of a phyloseq object. Function from the... |
| set_treatment_levels | set_treatment_levels |
| soil_column | Soil Column 16S Data - OTUs |
| taxa_abundance_bars | Create a ggplot object of the abundance barplots from a... |
| taxa_core | Filter taxa in phyloseq-object to only include core taxa.... |
| taxa_core_graph | Create graph of the core taxa seen in phyloseq-object over a... |
| taxa_extract | Extracts specific taxa from all samples based on a given... |
| taxa_filter | Filter taxa based on proportion of samples they are observed... |
| taxa_proportions | Compute proportions for taxa. |
| taxa_prune | Remove specific taxa from all samples based on a given... |
| tsne_phyloseq | Create a ggplot object using t-SNE from a phyloseq object.... |
| unique_taxa | Find unique taxa between treatments of a phyloseq object.... |
| variable_correlation | Computes the correlation of numerical variables with taxa... |
| variable_correlation_heatmap | Computes the correlation of numerical variables with taxa... |
| variable_correlation_network | Create a node network ggplot object of the correlation of... |
