Updated for Roxygen 7.3.0

smped · Feb 2, 2024 · 27b9538 · 27b9538
1 parent 96f1598
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ngsReports
-Version: 2.5.0
-Date: 2023/10/11
+Version: 2.5.1
+Date: 2024/02/02
 Title: Load FastqQC reports and other NGS related files
 Authors@R: c(
     person("Stevie", "Pederson", 
@@ -54,7 +54,7 @@ Imports:
     utils,
     zoo
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Collate: 
     'AllGenerics.R'
     'validationFunctions.R'

diff --git a/R/plotAdapterContent.R b/R/plotAdapterContent.R
@@ -435,7 +435,7 @@ setMethod(
 )
 #' @importFrom tidyr complete unnest
 #' @importFrom dplyr summarise group_by bind_rows
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #' @importFrom tidyselect any_of
 #' @rdname plotAdapterContent-methods
 #' @export

diff --git a/R/plotBaseQuals.R b/R/plotBaseQuals.R
@@ -83,7 +83,7 @@
 #' @import tibble
 #' @importFrom tidyr unnest
 #' @importFrom stringr str_split
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #'
 #' @name plotBaseQuals
 #' @rdname plotBaseQuals-methods
@@ -404,7 +404,7 @@ setMethod(
 )
 #' @importFrom tidyselect everything all_of
 #' @importFrom tidyr pivot_longer
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #' @rdname plotBaseQuals-methods
 #' @export
 setMethod(

diff --git a/R/plotDupLevels.R b/R/plotDupLevels.R
@@ -69,7 +69,7 @@
 #' @importFrom tidyselect contains
 #' @importFrom forcats fct_inorder
 #' @import tibble
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #'
 #' @name plotDupLevels
 #' @rdname plotDupLevels-methods
@@ -355,7 +355,7 @@ setMethod(
 }
 )
 #' @importFrom stats weighted.mean
-#' @importFrom rlang sym "!!"
+#' @importFrom rlang sym !!
 #' @importFrom dplyr group_by ungroup summarise
 #' @importFrom tidyr unnest
 #' @importFrom scales percent
@@ -475,7 +475,7 @@ setMethod(
   }
 )
 #' @importFrom tidyr unnest
-#' @importFrom rlang sym "!!"
+#' @importFrom rlang sym !!
 #' @importFrom dplyr group_by mutate summarise ungroup
 #' @importFrom grDevices colorRampPalette
 #' @importFrom stats weighted.mean

diff --git a/R/plotFastqcPCA.R b/R/plotFastqcPCA.R
@@ -38,7 +38,7 @@
 #' @importFrom scales percent
 #' @importFrom tidyr pivot_wider
 #' @importFrom zoo na.locf
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #' @import ggplot2
 #' @import tibble
 #'

diff --git a/R/plotGcContent.R b/R/plotGcContent.R
@@ -85,7 +85,7 @@
 #' @importFrom stats hclust dist
 #' @import ggplot2
 #' @importFrom stringr str_to_title
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #' @name plotGcContent
 #' @rdname plotGcContent-methods
 #' @export

diff --git a/R/plotInsertSize.R b/R/plotInsertSize.R
@@ -50,7 +50,7 @@ setGeneric(
   }
 )
 #' @importFrom tidyr unnest
-#' @importFrom rlang sym "!!"
+#' @importFrom rlang sym !!
 #' @rdname plotInsertSize-methods
 #' @export
 setMethod(
@@ -139,7 +139,7 @@ setMethod(
   }
 )
 #' @importFrom tidyr unnest
-#' @importFrom rlang sym "!!"
+#' @importFrom rlang sym !!
 #' @importFrom scales percent comma
 #' @rdname plotInsertSize-methods
 #' @export

diff --git a/R/plotKmers.R b/R/plotKmers.R
@@ -339,7 +339,7 @@ setMethod(
 
   }
 )
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #' @importFrom forcats fct_rev
 #' @importFrom dplyr reframe group_by bind_rows
 #' @rdname plotKmers-methods

diff --git a/R/plotNContent.R b/R/plotNContent.R
@@ -271,7 +271,7 @@ setMethod(
 #' @importFrom tidyr unnest
 #' @importFrom tidyselect any_of
 #' @importFrom scales label_percent comma
-#' @importFrom rlang sym "!!"
+#' @importFrom rlang sym !!
 #' @rdname plotNContent-methods
 #' @export
 setMethod(
@@ -376,7 +376,7 @@ setMethod(
 #' @importFrom tidyr unnest
 #' @importFrom tidyselect any_of
 #' @importFrom scales percent comma
-#' @importFrom rlang sym "!!"
+#' @importFrom rlang sym !!
 #' @rdname plotNContent-methods
 #' @export
 setMethod(

diff --git a/R/plotOverrep.R b/R/plotOverrep.R
@@ -59,7 +59,7 @@
 #'
 #' @importFrom plotly layout ggplotly
 #' @importFrom grDevices rgb
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #' @import ggplot2
 #'
 #' @name plotOverrep

diff --git a/R/plotSeqContent.R b/R/plotSeqContent.R
@@ -421,7 +421,7 @@ setMethod(
   }
 )
 #' @importFrom tidyr unnest pivot_longer
-#' @importFrom rlang sym "!!"
+#' @importFrom rlang sym !!
 #' @importFrom scales label_percent
 #' @rdname plotSeqContent-methods
 #' @export
@@ -624,6 +624,8 @@ setMethod(
         !!sym("reads"), all_of(bases), !!sym("position")
       )
       df[bases] <- lapply(df[bases], function(x) round(100 * x, 2))
+      if ("Module" %in% names(df))
+        df[["Module"]] <- factor(df[["Module"]], levels = mod)
 
       ## Round to 2 digits to reduce the complexity of the colour palette
       maxFreq <- max(unlist(df[bases]))

diff --git a/R/plotSeqLengthDistn.R b/R/plotSeqLengthDistn.R
@@ -69,7 +69,7 @@
 #' @importFrom tidyr pivot_wider complete nesting unnest
 #' @importFrom tidyselect everything any_of
 #' @importFrom grDevices hcl.colors
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #' @import ggplot2
 #'
 #' @name plotSeqLengthDistn

diff --git a/R/plotSeqQuals.R b/R/plotSeqQuals.R
@@ -62,7 +62,7 @@
 #' @importFrom scales percent comma percent_format
 #' @importFrom tidyr pivot_wider complete nesting
 #' @importFrom grDevices hcl.colors
-#' @importFrom rlang "!!" sym
+#' @importFrom rlang !! sym
 #' @import ggplot2
 #'
 #' @name plotSeqQuals

diff --git a/TODO.md b/TODO.md
@@ -1,9 +1,9 @@
 # TODO
 
 - [x] Check how themes are handled & use `theme_get()` as default if none supplied
+- [x] Ensure factor levels are correct for `Before_filtering` and `After_filtering`
 - [ ] Add line plot to `plotInsertSize()`
 - [ ] Add options to facet by base for `plotBaseQuals()` for a `FastpDataList` object
-- [ ] Ensure factor levels are correct for `Before_filtering` and `After_filtering`
 - [ ] Add Overrepresented Sequences for `FastpData` and `FastpDataList`
 - [ ] Build more plotting/reporting functions for fastp reports
 - [ ] Add methylation logs from SammyB

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,3 +1,7 @@
+Changes in version 2.5.1
++ Changed method for setting default theme using plotTheme
++ Set factor levels for plotSeqContent for FastpDataList
+
 Changes in version 2.3.5
 + added support for rnaseqc metrics files
 

diff --git a/man/plotAdapterContent-methods.Rd b/man/plotAdapterContent-methods.Rd
diff --git a/man/plotBaseQuals-methods.Rd b/man/plotBaseQuals-methods.Rd
diff --git a/man/plotDupLevels-methods.Rd b/man/plotDupLevels-methods.Rd
diff --git a/man/plotGcContent-methods.Rd b/man/plotGcContent-methods.Rd
diff --git a/man/plotInsertSize-methods.Rd b/man/plotInsertSize-methods.Rd
diff --git a/man/plotKmers-methods.Rd b/man/plotKmers-methods.Rd
diff --git a/man/plotNContent-methods.Rd b/man/plotNContent-methods.Rd
diff --git a/man/plotReadTotals-methods.Rd b/man/plotReadTotals-methods.Rd
diff --git a/man/plotSeqContent-methods.Rd b/man/plotSeqContent-methods.Rd