Man pages for leylabmpi/LeyLabRMisc
Ley Lab misc R functions, rmd templates, etc.

ancombc_tidyTidy ANCOM-BC output
ancombc_unbiased_abundancesGet unbiased abundances from ANCOM-BC output
as.Numconvert to numeric while avoiding factor conversion issues
bash_jobbash job using conda env
beta2mtxConvert tidy beta diversity table to a wide distance matrix
calc_alpha_divCalculate common alpha-diversity metrics You need the "vegan"...
calc_beta_divbeta-diversity calculation
calc_PCoAWrapper for cmdscale
calculate_rarefaction_curvesFunction for rarefaction analysis
cat_filepretty printing of a text file via cat
clustermq_get_logsGet/read clustermq cluster job log files
clustermq_logfileSet a path for clustermq cluster job log files
clustermq_setupSet clustermq options
condaInfo"conda list" in R
df.dimsChanging number of rows/columns shown when printing a data...
dfheadA simple dataframe summary
dist_formatcreating a string with distance & percent explained
dot-.add_columnsadding columns to a data.frame, as needed
dot-add_columnsadding columns to a data.frame, as needed
dot-ancombc_tidytidy ancom-bc output
dot-calc_pdcalculate Faith's PD
dot-flatten_nestedflatten a nested list; return a list
dot-get_brewer_palettegetting RColorBrewer entire palette
dot-HFEsupporting function for HFE
dot-rec_searchrecursive search in a nested list; return flattened list
dot-well384_indexmaking 384-well plate index
dot-well96_indexmaking a 96-well plate index
ena_get_filereportGet file reports via ENA Portal API
ena_get_search_fieldsGet possible search fields
estimate_rarified_richnessHelper Function for rarefaction analysis
estimate_richness_phyphyloseq::estimate_richness, but includes Faith's PD
expand.grid.lowerexpand.grid(), but just lower-triange comparisions
extract_pltdtExtract data from ggplot object
fig_uuidcreate UUID for figure file name
files_to_listconvert a vector of file paths into a named list
FreadSimple wrapper around data.table::fread
helloHello, World!
InitWrapper for calling other init functions
itol_boxplotcreate itol boxplot file
itol_colorstripCreate itol colorstrip file
itol_externalshapecreate itol external shape file
itol_heatmapcreate itol heatmap file
itol_multibarcreate itol multi-bar file
itol_simplebarcreate itol simple-bar file
itol_symbolcreate itol symbol file
list_fileslist.files with full.names=TRUE & recursive=TRUE
make_dirA helper function for creating a directory (recursively)
mgnify_getGet MGnify info via the API
mgnify_requestGET request from the ENA
mgnify_request_getGET request to MGnify API
mlr_boruta_filterCustom mlr filter for Boruta
mlr_getNestedTuneResultsOptPathDfVersion of getNestedTuneResultsOptPathDf that actually works
ml_tax_HFEHierarchical Feature Selection
overlapDetermine counts of setdiff, intersect, & union of 2 vectors...
path_get_labelsplitting path and returning just one item in the vector
pcoa2dfConvert PCoA object to a tidy dataframe
p.dimsGlobal change of plot size options
phyloseq2dfConvert a sub-object of a phyloseq object to a dataframe
phyloseq_rel_abundTransform abundances to relative
pipelineInfopipeline sessionInfo
Plotplot figure and save the figure grob object to a file at the...
qsave_objSimple function for serializing a distance matrix or list of...
read_brackenFunction for reading in a bracken taxonomy table
read_eggnog_mapperFunction for reading in eggnog-mapper annotations and...
readLinesTailRead the last N lines of a file
Robj_md5sumDump an R object as text to a temp file and get the md5sum of...
row_meansrowMeans that works inside a dplyr::mutate() call
row_sumsrowSums that works inside a dplyr::mutate() call
scale_color_allGreat a better coloring scheme for taxon abundance barcharts
scale_fill_allGreat a better coloring scheme for taxon abundance barcharts
send_emailA helper function to send an email via the mail bash cmd
size_objectsReturns the sizes of R objects
snakemakeInfosnakemake conda info
split_pathpython's os.path.split() for R
summary_xSummary for numeric vectors that includes sd and stderr
taxonomy_levelsA simple function that returns a vector of taxonomy levels
tidy_pcoaPCoA on a 'long' (tidy) tibble, and a long tibble is returned
to_rdsSave object as RDS, with name automatically defined
unique_nPretty print number of unique elements in a vector
well2indexConvert between wellID and column-num
write_tablewriting table convenience function
leylabmpi/LeyLabRMisc documentation built on Nov. 3, 2022, 3:45 p.m.