feat: geom_aggrcoverage (2)

R/geoms.R

@@ -7,6 +7,13 @@
 #' @name geom_aggrcoverage
 #' @rdname geom_aggrcoverage
 #' 
+#' @param mapping mapping
+#' @param data data
+#' @param ... ...
+#' @param ci ci
+#' @param na.rm na.rm
+#' @param show.legend show.legend
+#' @param inherit.aes inherit.aes
 #' @return A `ggplot` object`
 #'
 #' @import ggplot2
@@ -15,6 +22,7 @@
 #' library(rtracklayer)
 #' library(plyranges)
 #' library(ggplot2)
+#' library(purrr)
 #' TSSs_bed <- system.file("extdata", "TSSs.bed", package = "tidyCoverage")
 #' features <- list(
 #'     TSS_fwd = import(TSSs_bed) |> filter(strand == '+'), 

R/globals.R

@@ -1,5 +1,7 @@
 utils::globalVariables(c(
     ".",
+    "ci_low", 
+    "ci_high", 
     "coord", 
     "feature", 
     ".feature", 

README.md

@@ -52,9 +52,8 @@ CE |>
     filter(track %in% c('MNase', 'PolII')) |> 
     filter(features == 'TSSs') |> 
     aggregate() |> 
-    ggplot(aes(x = coord, y = mean, ymin = ci_low, ymax = ci_high, fill = track, col = track)) + 
-    geom_ribbon(aes(ymin = ci_low, ymax = ci_high, fill = track), alpha = 0.2) + 
-    geom_line(aes(col = track)) + 
+    ggplot() + 
+    geom_aggrcoverage(aes(col = track)) + 
     facet_grid(track ~ ., scales = "free") + 
     labs(x = 'Distance from TSS', y = 'Signal coverage') + 
     theme_bw() + 
@@ -68,8 +67,8 @@ CE |>
 ```r
 CoverageExperiment(tracks, GRanges("II:450001-455000")) |> 
     expand() |> 
-    ggplot(aes(x = coord, y = coverage)) + 
-        geom_col(aes(fill = track, col = track)) + 
+    ggplot() + 
+        geom_aggrcoverage(aes(col = track)) + 
         facet_grid(track~., scales = 'free') + 
         scale_x_continuous(expand = c(0, 0)) + 
         theme_bw() + 

vignettes/tidyCoverage.Rmd

@@ -417,7 +417,7 @@ AC |>
     facet_grid(features ~ .)
 ```
 
-Nearly there, few cosmethic changes and we are done! 
+Nearly there, few cosmetic changes and we are done! 
 
 ```{r}
 AC |>