Merge pull request #38 from SchlossLab/calc-rel-abun

Create function to calculate relative abundances

NAMESPACE

@@ -2,6 +2,7 @@
 
 export("%>%")
 export(.data)
+export(calc_relabun)
 export(close_enough)
 export(format_number)
 export(inline_hook)

NEWS.md

@@ -6,18 +6,19 @@
   level (e.g. genus, phylum, etc.) to enable comparing analyses at different 
   taxonomic resolutions, as seen in <https://doi.org/10.1128/mbio.03161-21> 
   (#37, @kelly-sovacool).
+- New function `calc_relabun()` calculates OTU relative abundances (#38, @kelly-sovacool).
 
 # schtools 0.2.1
 
-- Improvements to `parse_tax()` (#32, @kelly-sovacool)
+- Improvements to `parse_tax()` (#32, @kelly-sovacool).
     - New column `label_html` provides HTML to correctly italicize genus names but not OTU labels.
     - Added an example to the intro vignette to demonstrate using this feature with `ggtext`.
     - Changed taxonomy data frame column names to lowercase and reordered them.
-- Minor documentation improvements (#33, @kelly-sovacool)
+- Minor documentation improvements (#33, @kelly-sovacool).
 
 # schtools 0.1.1
 
-- Refactored `read_tax()` (#30, @kelly-sovacool)
+- Refactored `read_tax()` (#30, @kelly-sovacool).
     - New function `parse_tax()` to separate the logic of reading and parsing taxonomy files.
     - `read_tax()` now accepts a `sep` parameter to handle different delim file types (e.g. csv or tsv).
 - schtools now has a logo! (#31, @kelly-sovacool)

R/calculate.R

@@ -0,0 +1,30 @@
+
+#' Calculate OTU relative abundances from a shared file
+#'
+#' @param abs_abun_dat a data frame from reading in a [shared file](https://mothur.org/wiki/shared_file).
+#'   Should contain a `Group` column for sample names,
+#'   `Otu` columns for absolute counts of each OTU,
+#'   and rows as each sample.
+#'
+#' @return a new data frame with OTU relative abundances in long format.
+#' @export
+#' @author Kelly Sovacool \email{sovacool@@umich.edu}
+#'
+#' @examples
+#' shared_dat <- readr::read_tsv(system.file("extdata", "test.shared",
+#'   package = "schtools"
+#' ))
+#' shared_dat %>% calc_relabun()
+calc_relabun <- function(abs_abun_dat) {
+  count <- Group <- mutate <- otu <- rel_abun <- total_counts <- NULL
+  abs_abun_dat$total_counts <- rowSums(abs_abun_dat %>%
+    dplyr::select(dplyr::starts_with("Otu")))
+  rel_abun_dat <- abs_abun_dat %>%
+    dplyr::rename(sample = Group) %>%
+    tidyr::pivot_longer(dplyr::starts_with("Otu"),
+      names_to = "otu", values_to = "count"
+    ) %>%
+    dplyr::mutate(rel_abun = count / total_counts) %>%
+    dplyr::select(sample, otu, rel_abun)
+  return(rel_abun_dat)
+}

_pkgdown.yml

@@ -23,10 +23,11 @@ reference:
   - schtools
 - title: Microbiome
   desc: >
-    Read files & handle microbiome-related data.
+    Handle microbiome-related data.
   contents:
   - starts_with('read_')
   - starts_with('parse_')
+  - calc_relabun
   - pool_taxon_counts
 - title: R Markdown helpers
   desc: >

docs/dev/pkgdown.yml

@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   logo: logo.html
   introduction: introduction.html
-last_built: 2022-09-22T16:31Z
+last_built: 2022-09-26T21:08Z
 urls:
   reference: http://www.schlosslab.org/schtools/reference
   article: http://www.schlosslab.org/schtools/articles