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... |
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