join_metadata: Add metadata to long distance matrix

In harrietr: Wrangle Phylogenetic Distance Matrices and Other Utilities

Description

This functions takes the output from dist_long, plus a data.frame with metadata, and attaches it to the data.frame output from dist_long. It uses a column in the metadata data.frame as a key to join the two data.frames. So, it requires a column of data in the metadata data.frame to have same ID labels as those in the pairwise comparison table.

Usage

join_metadata(dist, meta, isolate = "ISOLATES", group = "CLUSTER",
  remove_ind = TRUE)

Arguments

dist	A data.frame produced by dist_long function
meta	A data.frame with one column of IDs that match the IDs in dist_long
isolate	A character string with the name of the column in the meta data.frame with the ID data
group	A character string with the name of column containing the grouping variable
remove_ind	A boolean whether to remove all non-essential columns

Details

The output from dist_long with an additional column containing a factor, with levels composed of joining the categories in the group colum of the metadata data.frame for each pairwise comparison. For example, if one row has distance between samples id1 and id2, and in the grouping column of the metadata id1 is identified as part of group 'A', and id2 is identified as part of group 'B', then the output from that row will 'AB'. If they were from the same group, say 'A', the output would be just 'A'. In this way it is easy to identify pairs of isolates that are from the same group, and pairs of isolates that are from different groups.

Examples

## Not run: 
data(woodmouse)
data(woodmouse_meta)
dist_df <- dist_long(woodmouse)
join_metadata(dist_df, woodmouse_meta, isolate = 'SAMPLE_ID', group = 'CLUSTER', remove_ind = TRUE)

## End(Not run)

Example output

Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
# A tibble: 105 x 3
   iso1    iso2  CLUSTER
   <chr>   <chr> <fct>  
 1 No304   No305 AB     
 2 No306   No305 AB     
 3 No0906S No305 AB     
 4 No0908S No305 AB     
 5 No0909S No305 AC     
 6 No0910S No305 AB     
 7 No0912S No305 AC     
 8 No0913S No305 AB     
 9 No1103S No305 AC     
10 No1007S No305 AC     
# … with 95 more rows
Warning message:
`funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 

harrietr documentation built on May 2, 2019, 3:37 p.m.