Merge pull request #44 from SchlossLab/ggplot2-3.4.0

Fixes for ggplot2 v3.4.0 & tidyselect v1.2.0

.Rbuildignore

@@ -14,3 +14,4 @@
 ^_pkgdown\.yml$
 ^pkgdown$
 ^CRAN-SUBMISSION$
+^conda-env

.github/workflows/test-coverage.yml

@@ -13,9 +13,9 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |

NEWS.md

@@ -1,6 +1,6 @@
 # schtools development version
 
-- Preemptively fix test failure in advance of next ggplot2 release (#41, @kelly-sovacool).
+- Fixes for API changes in ggplot2 v3.4.0 and tidyselect v1.2.0 (#42, #44, @kelly-sovacool).
 
 # schtools 0.3.0
 

R/plot.R

@@ -64,7 +64,7 @@ theme_lucas <- function() {
       panel.background = ggplot2::element_blank(),
       legend.position = "bottom",
       legend.key = ggplot2::element_rect(
-        fill = "white", color = "white", size = 4
+        fill = "white", color = "white", linewidth = 4
       ),
       legend.key.width = ggplot2::unit(2, "cm"),
       legend.text = ggplot2::element_text(size = 12),

R/read_dist.R

@@ -14,6 +14,7 @@
 #' dist_tbl <- read_dist(dist_filepath)
 #' head(dist_tbl)
 read_dist <- function(dist_filename) {
+  distances <- rows <- NULL
   # TODO: input validation - make sure file has expected format & throw errors if it doesn't
   # read in the first row to determine the matrix dimensions
   matrix_dim <-
@@ -31,10 +32,10 @@ read_dist <- function(dist_filename) {
   return(
     distance_matrix %>%
       tidyr::pivot_longer(
-        cols = -.data[["rows"]],
+        cols = -rows,
         values_to = "distances",
         names_to = "columns"
       ) %>%
-      dplyr::filter(!is.na(.data[["distances"]]))
+      dplyr::filter(!is.na(distances))
   )
 }

R/read_tax.R

@@ -15,58 +15,60 @@
 #' head(taxonomy_tbl)
 parse_tax <- function(dat) {
   levels <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus")
-  dat <- dat %>%
-    dplyr::mutate(Taxonomy = gsub("_", " ", .data[["Taxonomy"]])) %>%
-    tidyr::separate(.data[["Taxonomy"]], levels, sep = "\\(\\d{2,3}\\);", extra = "drop") %>%
-    dplyr::select(-.data[["Size"]])
+  Classification <- Genus <- Level <- Lowest_classified <- OTU <- Size <- Taxonomy <- tax_otu_label <- NULL
+  dat_sep <- dat %>%
+    dplyr::mutate(Taxonomy = gsub("_", " ", Taxonomy)) %>%
+    tidyr::separate(Taxonomy, levels, sep = "\\(\\d{2,3}\\);", extra = "drop") %>%
+    dplyr::select(-Size)
   # in older version of mothur unclassified are listed as unclassified
   # without information from higher level classification
   # for those cases, append with lowest identified classification
-  if (any(dat$Genus == "unclassified")) {
-    dat <- dat %>%
+  if ("unclassified" %in% (dat_sep %>% dplyr::pull("Genus"))) {
+    dat_sep <- dat_sep %>%
       tidyr::pivot_longer(
-        cols = -.data[["OTU"]],
+        cols = -OTU,
         names_to = "Level",
         values_to = "Classification"
       ) %>%
       # order classification level
-      dplyr::mutate(Level = factor(.data[["Level"]], levels)) %>%
-      dplyr::left_join(dplyr::group_by(., .data[["OTU"]]) %>%
-        dplyr::filter(.data[["Classification"]] != "unclassified") %>%
-        # select lowest level classification
-        dplyr::filter(.data[["Level"]] == levels[max(as.numeric(.data[["Level"]]))]) %>%
-        dplyr::select(.data[["OTU"]], Lowest_classified = .data[["Classification"]]),
-      by = "OTU"
+      dplyr::mutate(Level = factor(Level, levels)) %>%
+      dplyr::left_join(
+        dplyr::group_by(., OTU) %>%
+          dplyr::filter(Classification != "unclassified") %>%
+          # select lowest level classification
+          dplyr::filter(Level == levels[max(as.numeric(Level))]) %>%
+          dplyr::select(OTU, Lowest_classified = Classification),
+        by = "OTU"
       ) %>%
-      dplyr::mutate(Classification = ifelse(.data[["Classification"]] == "unclassified",
+      dplyr::mutate(Classification = ifelse(Classification == "unclassified",
         # append unclassified with lowest classification
-        paste(.data[["Lowest_classified"]], .data[["Classification"]], sep = " "),
-        .data[["Classification"]]
+        paste(Lowest_classified, Classification, sep = " "),
+        Classification
       )) %>%
-      dplyr::select(-.data[["Lowest_classified"]]) %>%
+      dplyr::select(-Lowest_classified) %>%
       tidyr::pivot_wider(
         names_from = "Level",
         values_from = "Classification"
       )
   }
   # create label options for OTU and lowest taxonomic classification with the OTU
-  dat <- dat %>%
+  dat_labs <- dat_sep %>%
     dplyr::mutate(
-      tax_otu_label = paste0(.data[["Genus"]], " (", gsub("tu0*", "TU ", .data[["OTU"]]), ")"),
-      tax_otu_label = gsub(" unclassified", "", .data[["tax_otu_label"]]),
-      otu_label = paste0(gsub("tu0*", "TU ", .data[["OTU"]])),
+      tax_otu_label = paste0(Genus, " (", gsub("tu0*", "TU ", OTU), ")"),
+      tax_otu_label = gsub(" unclassified", "", tax_otu_label),
+      otu_label = paste0(gsub("tu0*", "TU ", OTU)),
       label_html = stringr::str_replace(
-        .data[["tax_otu_label"]],
+        tax_otu_label,
         "([a-zA-Z]+) (.*)",
         glue::glue("<i>\\1</i> \\2")
       )
     )
-  colnames(dat) <- tolower(colnames(dat))
-  dat <- dat %>%
+  colnames(dat_labs) <- tolower(colnames(dat_labs))
+  dat_reordered <- dat_labs %>%
     dplyr::relocate(c("otu_label", "tax_otu_label", "label_html"),
       .after = "otu"
     )
-  return(dat)
+  return(dat_reordered)
 }
 
 #' Read in a taxonomy file and parse it to a wide dataframe

conda-env/schtools-dev.yml

@@ -0,0 +1,26 @@
+name: schtools-dev
+channels:
+  - conda-forge
+  - r
+dependencies:
+  - r-base=4
+  - r-devtools
+  - r-dplyr
+  - r-formatR
+  - r-glue
+  - r-rlang
+  - r-stringr
+  - r-tidyr
+  - r-covr
+  - r-cowplot
+  - r-ggplot2=3.4.0
+  - r-ggtext
+  - r-here
+  #- r-hexSticker
+  - r-hrbrthemes
+  - r-knitr
+  - r-purrr
+  - r-readr
+  - r-rmarkdown
+  - r-showtext
+  - r-testthat 

docs/dev/pkgdown.yml

@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   logo: logo.html
   introduction: introduction.html
-last_built: 2022-10-11T16:57Z
+last_built: 2022-11-08T20:44Z
 urls:
   reference: http://www.schlosslab.org/schtools/reference
   article: http://www.schlosslab.org/schtools/articles

tests/testthat/test-read_dist.R

@@ -1,22 +1,24 @@
 test_that("read_dist works on example file", {
-  tbl_head <- structure(list(
-    rows = c("104_1_D1", "104_1_D10", "104_1_D10", "104_1_D2", "104_1_D2", "104_1_D2"),
-    columns = c("104_1_D0", "104_1_D0", "104_1_D1", "104_1_D0", "104_1_D1", "104_1_D10"),
-    distances = c(0.892663, 0.253927, 0.921823, 0.874497, 0.108682, 0.90357)
-  ),
-  row.names = c(NA, -6L),
-  class = c("tbl_df", "tbl", "data.frame")
+  tbl_head <- structure(
+    list(
+      rows = c("104_1_D1", "104_1_D10", "104_1_D10", "104_1_D2", "104_1_D2", "104_1_D2"),
+      columns = c("104_1_D0", "104_1_D0", "104_1_D1", "104_1_D0", "104_1_D1", "104_1_D10"),
+      distances = c(0.892663, 0.253927, 0.921823, 0.874497, 0.108682, 0.90357)
+    ),
+    row.names = c(NA, -6L),
+    class = c("tbl_df", "tbl", "data.frame")
   )
-  tbl_tail <- structure(list(
-    rows = c(
-      "98_3_Dminus1", "98_3_Dminus1", "98_3_Dminus1",
-      "98_3_Dminus1", "98_3_Dminus1", "98_3_Dminus1"
+  tbl_tail <- structure(
+    list(
+      rows = c(
+        "98_3_Dminus1", "98_3_Dminus1", "98_3_Dminus1",
+        "98_3_Dminus1", "98_3_Dminus1", "98_3_Dminus1"
+      ),
+      columns = c("98_3_D4", "98_3_D5", "98_3_D6", "98_3_D7", "98_3_D8", "98_3_D9"),
+      distances = c(0.659194, 0.697918, 0.717304, 0.621887, 0.645434, 0.638572)
     ),
-    columns = c("98_3_D4", "98_3_D5", "98_3_D6", "98_3_D7", "98_3_D8", "98_3_D9"),
-    distances = c(0.659194, 0.697918, 0.717304, 0.621887, 0.645434, 0.638572)
-  ),
-  row.names = c(NA, -6L),
-  class = c("tbl_df", "tbl", "data.frame")
+    row.names = c(NA, -6L),
+    class = c("tbl_df", "tbl", "data.frame")
   )
   dist_out <- read_dist(system.file("extdata",
     "sample.final.thetayc.0.03.lt.ave.dist",

tests/testthat/test-read_tax.R

@@ -1,8 +1,11 @@
-test_that("read_tax works on example file", {
-  taxonomy_out <- read_tax(system.file("extdata",
-    "test.taxonomy",
-    package = "schtools"
-  ))
+tax_infilename <- system.file("extdata",
+  "test.taxonomy",
+  package = "schtools"
+)
+tax_raw_tbl <- readr::read_tsv(tax_infilename)
+
+test_that("parse_tax works on example file", {
+  taxonomy_out <- parse_tax(tax_raw_tbl)
   expect_equal(
     colnames(taxonomy_out),
     c(
@@ -32,3 +35,9 @@ test_that("read_tax works on example file", {
     )
   )
 })
+test_that("read_tax works as well as `read_tsv %>% parse_tax`", {
+  expect_equal(
+    read_tax(tax_infilename),
+    parse_tax(tax_raw_tbl)
+  )
+})