fix indents and length of lines

waldronlab · Apr 8, 2024 · 338836a · 338836a
1 parent 4040b28
commit 338836a
Show file tree

Hide file tree

Showing 10 changed files with 872 additions and 788 deletions.
diff --git a/R/bacdive.R b/R/bacdive.R
diff --git a/R/bugphyzz.R b/R/bugphyzz.R
diff --git a/R/cache.R b/R/cache.R
@@ -8,25 +8,25 @@
     res <- BiocFileCache::bfcquery(cache, rname, "rname", exact = TRUE)
     rid <- res$rid
     if (length(rid) > 0 && force) {
-      time <- res$create_time
-      if (verbose) {
-        message('Replacing previous version downloaded on ', time, '.')
-      }
-      BiocFileCache::bfcremove(cache, rid)
-      rid <- names(BiocFileCache::bfcadd(cache, rname, url))
+        time <- res$create_time
+        if (verbose) {
+            message('Replacing previous version downloaded on ', time, '.')
+        }
+        BiocFileCache::bfcremove(cache, rid)
+        rid <- names(BiocFileCache::bfcadd(cache, rname, url))
     }
     if (!length(rid)) {
-      if (verbose) {
-        message( "Downloading, ", rname, ".")
-      }
-      rid <- names(BiocFileCache::bfcadd(cache, rname, url))
+        if (verbose) {
+            message( "Downloading, ", rname, ".")
+        }
+        rid <- names(BiocFileCache::bfcadd(cache, rname, url))
     }
     time <- BiocFileCache::bfcinfo(cache, rid)$create_time
     message('Using data downloaded on ', time, '.')
     BiocFileCache::bfcrpath(cache, rids = rid)
 }
 
 .removeCache <- function() {
-  cache <- .getCache()
-  BiocFileCache::removebfc(cache)
+    cache <- .getCache()
+    BiocFileCache::removebfc(cache)
 }
diff --git a/R/fattyAcidComposition.R b/R/fattyAcidComposition.R
@@ -4,34 +4,38 @@
 ## TODO Names of the Fatty Acids should be more "user-friendly"
 ## TODO Maybe a threshold should be decided to consider a FA as present or not.
 .fattyAcidComposition <- function(){
-  link <- .customLinks() |>
-    dplyr::filter(functionname == "fattyAcidComposition") |>
-    dplyr::pull(link)
-  fac_wide <- utils::read.csv(link, check.names = FALSE)
-  fac_long <- fac_wide |>
-    tidyr::pivot_longer(
-      cols = `Br-C10:1`:`Oxo-C19:1`,
-      names_to = "Attribute_new", values_to = "Attribute_value"
-  ) |>
-    dplyr::mutate(NCBI_ID = as.character(NCBI_ID))
-  dplyr::left_join(fac_long, ranks_parents, by = "NCBI_ID") |>
-    as.data.frame() |>
-    .addSourceInfo() |>
-    purrr::modify_at(
-      .at = c('Attribute', 'Frequency', 'Evidence', 'Confidence_in_curation'),
-      .f = ~ stringr::str_to_lower(.x)
-    ) |>
-    dplyr::select(-Attribute) |>
-    dplyr::rename(Attribute = Attribute_new) |>
-    .reorderColumns(attr_type = 'numeric')
+    link <- .customLinks() |>
+        dplyr::filter(functionname == "fattyAcidComposition") |>
+        dplyr::pull(link)
+    fac_wide <- utils::read.csv(link, check.names = FALSE)
+    fac_long <- fac_wide |>
+        tidyr::pivot_longer(
+            cols = `Br-C10:1`:`Oxo-C19:1`,
+            names_to = "Attribute_new", values_to = "Attribute_value"
+        ) |>
+        dplyr::mutate(NCBI_ID = as.character(NCBI_ID))
+    dplyr::left_join(fac_long, ranks_parents, by = "NCBI_ID") |>
+        as.data.frame() |>
+        .addSourceInfo() |>
+        purrr::modify_at(
+            .at = c(
+                'Attribute', 'Frequency', 'Evidence', 'Confidence_in_curation'
+            ),
+            .f = ~ stringr::str_to_lower(.x)
+        ) |>
+        dplyr::select(-Attribute) |>
+        dplyr::rename(Attribute = Attribute_new) |>
+        .reorderColumns(attr_type = 'numeric')
 }
 
 ## Function to import custom links
 .customLinks <- function(keyword = "all"){
     fname <-
         system.file("extdata/spreadsheet_customlinks.tsv", package = "bugphyzz")
     links <- utils::read.table(fname, sep = '\t', header = TRUE)
-    ifelse(keyword[1] == "all", links, links <-
-                      links[links$physiology %in% keyword,])
+    ifelse(
+        keyword[1] == "all", links,
+        links <- links[links$physiology %in% keyword,]
+    )
     links
 }