Miscellaneous R functions, with a focus on microbiome data analysis. Inspired by kylebittinger/kylemisc.

See the docs for more info.

Help topics

  • agglomerate
    Agglomerates the sample metadata, counts, and taxa info into one melted df.
  • blast6_colnames
    Default BLAST outfmt 6 column names
  • contam_test
    Test for an OTU's (inverse) correlation between its abundance and amplicon concentration.
  • dynamic_chunk
    Creates a chunk for a plot with a given figure height and width.
  • heatmap_dims
    Find the dimensions of a ggplot2 heatmap.
  • make_square
    Uses the number of columns and number of rows in a heatmap to fix the
  • Mode
    Find the mode of a logical or numeric vector
  • na_zeros
    Set zeros to NA
  • named_vector
    Create a named vector using the values from one column in the second.
  • polyatest
    Uses a Dirichlet multinomial distribution to test for OTUs in the first
  • read_blast6
    Reads an output file from BLAST in the outfmt=6 format (tab delimited)
  • reorder_taxa
    Reorder levels of subtaxa by parent taxa
  • saturated_rainbow_cts
    Saturated rainbow for counts
  • saturated_rainbow_pct
    Saturated rainbow for proportions
  • subcolor_pal
    Grouped color palette for factors
  • subset_matrix
    Subset a (counts) matrix based on the column from a dataframe.
  • tax_climber
    Finds the lowest taxonomic rank that isn't NA, stopping at `end`.


  • Imports: dplyr, broom, lazyeval, purrr, qiimer, tidyr
  • Suggests: knitr, ggplot2, polyafit