Properly address id column

R/geom_gene.R

@@ -257,7 +257,7 @@ makeContent.genetree <- function(x) {
   cds_data <- data %>% filter(.data$type == "CDS")
   if (nrow(cds_data) > 0) {
     cds_exons <- cds_data %>%
-      dplyr::group_by(id) %>%
+      dplyr::group_by(.data$id) %>%
       dplyr::summarize(
         dplyr::across(c(-.data$x, -.data$xend, -.data$y), first),
         exons = list(exon_polys(.data$x, .data$xend, .data$y, height, arrow_width, arrow_height))
@@ -269,7 +269,7 @@ makeContent.genetree <- function(x) {
   rna_data <- data %>% filter(.data$type != "CDS")
   if (nrow(rna_data) > 0) {
     rna_exons <- rna_data %>%
-      dplyr::group_by(id) %>%
+      dplyr::group_by(.data$id) %>%
       dplyr::summarize(
         dplyr::across(c(-.data$x, -.data$xend, -.data$y), first),
         exons = list(exon_polys(.data$x, .data$xend, .data$y, rna_height, rna_arrow_width, rna_arrow_height))
@@ -290,7 +290,7 @@ makeContent.genetree <- function(x) {
       dplyr::group_by(.data$group) %>%
       # remove CDS if group has mRNA
       dplyr::filter(.data$type != (if ("mRNA" %in% .data$type) "CDS" else "!bogus")) %>%
-      dplyr::group_by(id) %>%
+      dplyr::group_by(.data$id) %>%
       dplyr::filter(n() > 1) %>%
       dplyr::summarize(
         dplyr::across(c(-.data$x, -.data$xend, -.data$y), first),

R/position_strandpile.R

@@ -125,15 +125,15 @@ PositionStrandpile <- ggproto("PositionStrandpile", Position,
     } else if (params$grouped) { # i.e. multi-exon as one unit
       # not pretty, but works for now
       data_grouped <- data %>%
-        dplyr::group_by(y, group) %>%
+        dplyr::group_by(.data$y, .data$group) %>%
         dplyr::summarize(
           start = min(x, xend) + 1, end = max(x, xend), is_reverse = ifelse(params$strandwise,
             xor(min(x) > max(xend), params$flip), params$flip
           )
         )
 
       data_grouped <- data_grouped %>%
-        dplyr::group_by(y, is_reverse) %>%
+        dplyr::group_by(.data$y, .data$is_reverse) %>%
         dplyr::mutate(yoff = (params$base + params$offset *
           stack_pos(start, end, params$gap)) *
           ifelse(is_reverse, -1, 1)) %>%
@@ -146,7 +146,7 @@ PositionStrandpile <- ggproto("PositionStrandpile", Position,
           start = pmin(x, xend) + 1, end = pmax(x, xend),
           is_reverse = if (params$strandwise) xor(x > xend, params$flip) else params$flip
         ) %>%
-        dplyr::group_by(y, is_reverse) %>%
+        dplyr::group_by(.data$y, .data$is_reverse) %>%
         dplyr::mutate(yoff = (params$base + params$offset *
           stack_pos(start, end, params$gap)) *
           ifelse(is_reverse, -1, 1)) %>%

R/read.R

@@ -258,7 +258,7 @@ filter_def_formats <- function(ff, format = NULL, context = NULL, parser = NULL)
     if (!is.null(context)) {
       # context=NA defines fallback parser which is always last in arrange
       ff <- ff %>%
-        dplyr::group_by(format) %>%
+        dplyr::group_by(.data$format) %>%
         dplyr::filter(context %in% !!context | is.na(context)) %>%
         dplyr::arrange(context, .by_group = TRUE) %>%
         slice_head(n = 1)