Function reference • sourmashconsumr

All functions

check_and_edit_names_in_signatures_df(): Check for missing name, NAs in name, or empty name in a data frame of signatures

check_compare_df_sample_col_and_move_to_rowname(): Internal function to check if the sample name is a column or a rowname and move it to a rowname if it is a column.

check_file_and_url_one(): Check if local file path or URL are valid

check_uniform_parameters_in_signatures_df(): Check uniformity in sketch parameters

from_gather_to_upset_df(): Convert a data frame containing sourmash gather results into a upset plot compatible data frame

from_list_to_upset_df(): Convert a list of vectors into an upset plot-compatible data.frame while conserving value names as row.names

from_signatures_to_rarefaction_df(): Create a tidy data.frame representing per-sample rarefaction information

from_signatures_to_upset_df(): Convert a data.frame containing hashes from many sourmash signatures into a upset plot compatible data.frame

from_taxonomy_annotate_to_count_table(): Transform the output of sourmash taxonomy annotate into a phyloseq OTU table (count table)

from_taxonomy_annotate_to_metacoder(): Transform the output of sourmash taxonomy annotate into a taxmap metacoder object

from_taxonomy_annotate_to_multi_strains(): Detect whether multiple strains of the same species are present in a sample.

from_taxonomy_annotate_to_phyloseq(): Transform the output of sourmash taxonomy annotate into a phyloseq object

from_taxonomy_annotate_to_tax_table(): Transform the output of sourmash taxonomy annotate into a phyloseq tax table

from_taxonomy_annotate_to_upset_inputs(): Transform a taxonomy annotate data frame into an upset plot compliant data frame

from_upset_df_to_intersection_members(): Extract the lineages that underlie the intersections in an upset plot

from_upset_df_to_intersection_summary(): Summarize the size of intersections between samples in an upset compliant data frame

from_upset_df_to_intersections(): Transform an upset compliant data frame into a data frame of intersection names and lineages

get_scaled_for_max_hash(): Calculate the scaled value for a signature from the max_hash value

gut_compare_df: Gut microbiome sourmash compare data frame

gut_gather_df: Gut microbiome sourmash gather data frame

gut_signatures_df: Gut microbiome sourmash signatures data frame

gut_taxonomy_annotate_df: Gut microbiome sourmash taxonomy annotate data frame

make_agglom_cols(): Helper function to define column names for taxonomy agglomeration

make_compare_mds(): Perform an MDS analysis from a sourmash compare output and produce a tidy data.frame

make_expression(): Make an expression vector for italicizing a subset of a vector

pivot_wider_taxonomy_annotate(): Pivot sourmash_taxonomy_results to wide format

plot_compare_heatmap(): Plot a heatmap from a tibble of sourmash compare results.

plot_compare_mds(): Plot an MDS data.frame produced from the output of sourmash compare

plot_gather_classified(): Visualize the classified and unclassified fraction of many samples using sourmash gather results.

plot_gather_upset(): Visualize the intersection of genome accessions in sourmash gather results from many samples

plot_signatures_rarefaction(): Plot a rarefaction curve to determine sequence saturation

plot_signatures_upset(): Visualize the intersection of minhashes in sourmash signatures from many samples

plot_taxonomy_annotate_sankey(): Visualize a sankey diagram from taxonomic lineages from one or many samples

plot_taxonomy_annotate_ts_alluvial(): Visualize an allivual flow plot from taxonomic lineages from one or many samples

plot_taxonomy_annotate_upset(): Visualize an upset plot of taxonomic lineage intersections between samples

read_compare_csv(): Read a CSV file output by sourmash compare

read_gather(): Read CSV file or files output by sourmash gather

read_signature(): Read sourmash signature or signatures into a dataframe

read_signature_one(): Read one sourmash signature into a dataframe

read_taxonomy_annotate(): Read CSV file or files output by sourmash taxonomy annotate

tax_glom_taxonomy_annotate(): Agglomerate counts of same lineage to specified level of taxonomy.

warning_handler(): Warning handler to suppress warning message that contains "The following named parsers don't match the column names:"