Man pages for eclarke/eclectic
Miscellaneous functions for bioinformatics data

agglomerateAgglomerates the sample metadata, counts, and taxa info into...
blast6_colnamesDefault BLAST outfmt 6 column names
contam_testTest for an OTU's (inverse) correlation between its abundance...
counts_matrixCreates a counts matrix from an agglomerated data frame.
dynamic_chunkCreates a chunk for a plot with a given figure height and...
heatmap_dimsFind the dimensions of a ggplot2 heatmap.
MakeHeatmapDataPrepare agglomerated dataframe for heatmap display.
make_squareUses the number of columns and number of rows in a heatmap to...
MakeUnifracDataCalculates the generalized UniFrac distances for an...
min_rankCreates a MinRank vector from an agglomerated data frame.
ModeFind the mode of a logical or numeric vector
named_vectorCreate a named vector using the values from one column in the...
na_zerosSet zeros to NA
PlotHeatmapPlot a standard rainbow heatmap with faceting.
polyatestUses a Dirichlet multinomial distribution to test for OTUs in...
prune_treePrunes a tree to only include specified OTUs.
read_blast6Reads an output file from BLAST in the outfmt=6 format (tab...
reorder_taxaReorder levels of subtaxa by parent taxa
root_treeRoot a tree using a random node as the root.
saturated_rainbow_ctsSaturated rainbow for counts
saturated_rainbow_pctSaturated rainbow for proportions
subcolor_palGrouped color palette for factors
subset_matrixSubset a (counts) matrix based on the column from a...
tax_climberFinds the lowest taxonomic rank that isn't NA, stopping at...
eclarke/eclectic documentation built on July 15, 2017, 2:12 a.m.