Man pages for leylabmpi/LeyLabRMisc
Ley Lab misc R functions, rmd templates, etc.
| ancombc_tidy | Tidy ANCOM-BC output |
| ancombc_unbiased_abundances | Get unbiased abundances from ANCOM-BC output |
| as.Num | convert to numeric while avoiding factor conversion issues |
| bash_job | bash job using conda env |
| beta2mtx | Convert tidy beta diversity table to a wide distance matrix |
| calc_alpha_div | Calculate common alpha-diversity metrics You need the "vegan"... |
| calc_beta_div | beta-diversity calculation |
| calc_PCoA | Wrapper for cmdscale |
| calculate_rarefaction_curves | Function for rarefaction analysis |
| cat_file | pretty printing of a text file via cat |
| clustermq_get_logs | Get/read clustermq cluster job log files |
| clustermq_logfile | Set a path for clustermq cluster job log files |
| clustermq_setup | Set clustermq options |
| condaInfo | "conda list" in R |
| df.dims | Changing number of rows/columns shown when printing a data... |
| dfhead | A simple dataframe summary |
| dist_format | creating a string with distance & percent explained |
| dot-.add_columns | adding columns to a data.frame, as needed |
| dot-add_columns | adding columns to a data.frame, as needed |
| dot-ancombc_tidy | tidy ancom-bc output |
| dot-calc_pd | calculate Faith's PD |
| dot-flatten_nested | flatten a nested list; return a list |
| dot-get_brewer_palette | getting RColorBrewer entire palette |
| dot-HFE | supporting function for HFE |
| dot-rec_search | recursive search in a nested list; return flattened list |
| dot-well384_index | making 384-well plate index |
| dot-well96_index | making a 96-well plate index |
| ena_get_filereport | Get file reports via ENA Portal API |
| ena_get_search_fields | Get possible search fields |
| estimate_rarified_richness | Helper Function for rarefaction analysis |
| estimate_richness_phy | phyloseq::estimate_richness, but includes Faith's PD |
| expand.grid.lower | expand.grid(), but just lower-triange comparisions |
| extract_pltdt | Extract data from ggplot object |
| fig_uuid | create UUID for figure file name |
| files_to_list | convert a vector of file paths into a named list |
| Fread | Simple wrapper around data.table::fread |
| hello | Hello, World! |
| Init | Wrapper for calling other init functions |
| itol_boxplot | create itol boxplot file |
| itol_colorstrip | Create itol colorstrip file |
| itol_externalshape | create itol external shape file |
| itol_heatmap | create itol heatmap file |
| itol_multibar | create itol multi-bar file |
| itol_simplebar | create itol simple-bar file |
| itol_symbol | create itol symbol file |
| list_files | list.files with full.names=TRUE & recursive=TRUE |
| make_dir | A helper function for creating a directory (recursively) |
| mgnify_get | Get MGnify info via the API |
| mgnify_request | GET request from the ENA |
| mgnify_request_get | GET request to MGnify API |
| mlr_boruta_filter | Custom mlr filter for Boruta |
| mlr_getNestedTuneResultsOptPathDf | Version of getNestedTuneResultsOptPathDf that actually works |
| ml_tax_HFE | Hierarchical Feature Selection |
| overlap | Determine counts of setdiff, intersect, & union of 2 vectors... |
| path_get_label | splitting path and returning just one item in the vector |
| pcoa2df | Convert PCoA object to a tidy dataframe |
| p.dims | Global change of plot size options |
| phyloseq2df | Convert a sub-object of a phyloseq object to a dataframe |
| phyloseq_rel_abund | Transform abundances to relative |
| pipelineInfo | pipeline sessionInfo |
| Plot | plot figure and save the figure grob object to a file at the... |
| qsave_obj | Simple function for serializing a distance matrix or list of... |
| read_bracken | Function for reading in a bracken taxonomy table |
| read_eggnog_mapper | Function for reading in eggnog-mapper annotations and... |
| readLinesTail | Read the last N lines of a file |
| Robj_md5sum | Dump an R object as text to a temp file and get the md5sum of... |
| row_means | rowMeans that works inside a dplyr::mutate() call |
| row_sums | rowSums that works inside a dplyr::mutate() call |
| scale_color_all | Great a better coloring scheme for taxon abundance barcharts |
| scale_fill_all | Great a better coloring scheme for taxon abundance barcharts |
| send_email | A helper function to send an email via the mail bash cmd |
| size_objects | Returns the sizes of R objects |
| snakemakeInfo | snakemake conda info |
| split_path | python's os.path.split() for R |
| summary_x | Summary for numeric vectors that includes sd and stderr |
| taxonomy_levels | A simple function that returns a vector of taxonomy levels |
| tidy_pcoa | PCoA on a 'long' (tidy) tibble, and a long tibble is returned |
| to_rds | Save object as RDS, with name automatically defined |
| unique_n | Pretty print number of unique elements in a vector |
| well2index | Convert between wellID and column-num |
| write_table | writing table convenience function |
