diff --git a/R/geoms.R b/R/geoms.R index 6addb4a..88766d5 100644 --- a/R/geoms.R +++ b/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 == '+'), diff --git a/R/globals.R b/R/globals.R index d8138d6..d5f7791 100644 --- a/R/globals.R +++ b/R/globals.R @@ -1,5 +1,7 @@ utils::globalVariables(c( ".", + "ci_low", + "ci_high", "coord", "feature", ".feature", diff --git a/README.md b/README.md index 00ea877..6bf1cac 100644 --- a/README.md +++ b/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() + diff --git a/man/geom_aggrcoverage.Rd b/man/geom_aggrcoverage.Rd index 73a9a16..50c39b5 100644 --- a/man/geom_aggrcoverage.Rd +++ b/man/geom_aggrcoverage.Rd @@ -14,6 +14,21 @@ geom_aggrcoverage( inherit.aes = TRUE ) } +\arguments{ +\item{mapping}{mapping} + +\item{data}{data} + +\item{...}{...} + +\item{ci}{ci} + +\item{na.rm}{na.rm} + +\item{show.legend}{show.legend} + +\item{inherit.aes}{inherit.aes} +} \value{ A \code{ggplot} object` } @@ -27,6 +42,7 @@ A \code{ggplot} object` 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 == '+'), diff --git a/vignettes/tidyCoverage.Rmd b/vignettes/tidyCoverage.Rmd index 7d22690..36dda0f 100644 --- a/vignettes/tidyCoverage.Rmd +++ b/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 |>