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