Man pages for schuyler-smith/phyloschuyler
Functions to help analyze data as phyloseq objects

abundance_heatmapCreate a heatmap ggplot object of the abundance table from a...
abundance_linesCreate a lineplot ggplot object of the abundance table from a...
alpha_diversity_graphCreate a boxplot of the alpha-diversity. Function from the...
arrange_co_occurrence_tableArrange co-occurence table
assign_rankAssign rank values to a matrix.
check_index_classificationConverts numeric values to column names in tax_table
check_index_treatmentConverts numeric values to column names in sample_data.
check_TaRphyloseq object so taxa are rows.
CI_ellipseCreates confidence interval ellipse for scatterplot
common_taxaFind taxa shared between treatments of a phyloseq object....
conglomerate_samplesMerge samples based on common factor within sample_data....
conglomerate_taxaConglomerate taxa by sample on a given classification level....
co_occurrencepair-wise Spearman rank co-occurrence, written in efficient...
co_occurrence_networkCreate a node network ggplot object of the co-occurrence from...
CorrelationCo-occurrence calculation
create_paletteCreates color palettes for figures.
curate_co_occurrenceCurate co-occurrence data. Function from the...
histogram_permuted_rhosCreate a ggplot object of the distribution of rho values from...
melt_phyloseqMelt a phyloseq object into a data.table. Function from the...
merge_treatmentsCombine meta-data columns. Function from the...
mock_phyloseqMock Phyloseq Object 1
mock_phyloseq_2Mock Phyloseq Object 2
network_layout_psCreate an layout_igraph object of the co-occurrence from a...
network_psCreate an igraph network object of the co-occurrence from a...
nmds_phyloseqCreate a ggplot object of the NMDS from a phyloseq object....
pcoa_phyloseqCreate a ggplot object of the PCoA from a phyloseq object....
permute_rhoPermutes the pair-wise Spearman rank co-occurrence, to...
permute_rho_RcppCo-occurrence rho calculations
phylogeny_profileCreate a ggplot object of the phylogenic barplots from a...
phylosmithphylosmith-package
quantile_permuted_rhosCalculate quantiles for the permuted rho values from the...
relative_abundanceTransform abundance data in an 'otu_table' to relative...
set_sample_orderRe-orders the samples of a phyloseq object. Function from the...
set_treatment_levelsset_treatment_levels
soil_columnSoil Column 16S Data - OTUs
taxa_abundance_barsCreate a ggplot object of the abundance barplots from a...
taxa_coreFilter taxa in phyloseq-object to only include core taxa....
taxa_core_graphCreate graph of the core taxa seen in phyloseq-object over a...
taxa_filterFilter taxa based on proportion of samples they are observed...
taxa_proportionsCompute proportions for taxa.
tsne_phyloseqCreate a ggplot object using t-SNE from a phyloseq object....
unique_taxaFind unique taxa between treatments of a phyloseq object....
variable_correlationComputes the correlation of numerical variables with taxa...
variable_correlation_heatmapComputes the correlation of numerical variables with taxa...
variable_correlation_networkCreate a node network ggplot object of the correlation of...
schuyler-smith/phyloschuyler documentation built on July 26, 2020, 4:56 p.m.