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v4: plots: call plotExpression for box and violin
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Signed-off-by: Daena Rys <[email protected]>
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@Daenarys8
Daenarys8 committed Aug 10, 2024
1 parent 73afd36 commit cea36d0
Showing 1 changed file with 86 additions and 72 deletions.
158 changes: 86 additions & 72 deletions R/plotAbundanceDensity.R
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Original file line number Diff line number Diff line change
Expand Up @@ -183,28 +183,48 @@ setMethod("plotAbundanceDensity", signature = c(x = "SummarizedExperiment"),
}
########################### Input Check end ############################
# Gets data that will be plotted. Gets a list
density_data_list <- .incorporate_density_data(object = x,
assay.type = assay.type,
n = n,
colour_by = colour.by,
shape_by = shape.by,
size_by = size.by,
order_descending = decreasing)
# Extracts the density data and aesthetic from the list
density_data <- density_data_list$density_data
colour_by <- density_data_list$colour_by
shape_by <- density_data_list$shape_by
size_by <- density_data_list$size_by

# Gets the plot from plotter
plot_out <- .density_plotter(density_data = density_data,
layout = layout,
xlab = assay.type,
colour_by = colour_by,
shape_by = shape_by,
size_by = size_by,
...)
return(plot_out)
if (layout %in% c("density", "point", "jitter")) {
density_data_list <- .incorporate_density_data(object = x,
assay.type = assay.type,
n = n,
colour_by = colour.by,
shape_by = shape.by,
size_by = size.by,
order_descending = decreasing)
# Extracts the density data and aesthetic from the list
density_data <- density_data_list$density_data
colour_by <- density_data_list$colour_by
shape_by <- density_data_list$shape_by
size_by <- density_data_list$size_by

# Gets the plot from plotter
plot_out <- .density_plotter(density_data = density_data,
layout = layout,
xlab = assay.type,
colour_by = colour_by,
shape_by = shape_by,
size_by = size_by,
...)
return(plot_out)
}
# Plot when layout is box
else if (layout == "box") {
top_taxa <- getTop(x, top = n, assay.type = assay.type)
plot_out <- plotExpression(x, features = top_taxa,
assay.type = assay.type, show_boxplot = TRUE, show_violin = FALSE, ...) +
ggplot2::coord_flip()
return(plot_out)
}
# Plot when layout is violin
else if (layout == "violin") {
top_taxa <- getTop(x, top = n, assay.type = assay.type)
plot_out <- plotExpression(x, features = top_taxa, assay.type = assay.type, ...) +
ggplot2::coord_flip()
return(plot_out)
}
else {
stop("Unsupported layout option: '", layout, "'.", call. = FALSE)
}
}
)

Expand Down Expand Up @@ -293,58 +313,52 @@ setMethod("plotAbundanceDensity", signature = c(x = "SummarizedExperiment"),
angle_x_text = angle.x.text,
angle.x.text = TRUE){
# start plotting
plot_out <- ggplot(density_data, aes(x = .data[["X"]])) +
xlab(xlab) +
ylab(ylab)

# Prepare arguments for different geoms
geom_args <- list()
if (layout == "density") {
geom_args <- .get_density_args(colour_by, alpha = point_alpha)
geom_args$args$mapping$y <- NULL # Density plots don't need y mapping
} else if (layout %in% c("point", "jitter", "box", "violin")) {
geom_args <- .get_point_args(
colour_by, shape_by = shape_by, size_by = size_by,
alpha = point_alpha, shape = point_shape,
size = point_size, colour = point_colour
)
geom_args$args$mapping$y <- sym("Y")
}
else {
stop("Unsupported layout option: '", layout, "'.", call. = FALSE)
}

# Add the appropriate geom to the plot
if (layout == "density") {
plot_out$data$Y <- factor(plot_out$data$Y, levels = rev(levels(plot_out$data$Y)))

grid_args <- list(switch = ifelse(flipped, "x", "y"), scales = ifelse(scales_free, "free", "fixed"))
if (flipped) {
grid_args$cols <- vars(!!sym("Y"))
} else {
grid_args$rows <- vars(!!sym("Y"))
}

plot_out <- ggplot(density_data, aes(x=.data[["X"]])) +
xlab(xlab) +
ylab(ylab)
# Layout can be "density", "jitter", or "point"
if (layout == "density"){
plot_out$data$Y <- factor(plot_out$data$Y,
levels = rev(levels(plot_out$data$Y)) )
point_args <- .get_density_args(colour_by,
alpha = point_alpha)
# density specific options for flipping
grid_args <- list(switch = ifelse(flipped, "x", "y"),
scales = ifelse(scales_free, "free", "fixed"))
if(flipped){
grid_args$cols <- vars(!!sym("Y"))
} else {
grid_args$rows <- vars(!!sym("Y"))
}
#
plot_out <- plot_out +
do.call(geom_density, point_args$args) +
do.call(facet_grid, grid_args)
shape_by <- NULL
size_by <- NULL
angle_x_text <- FALSE
} else if (layout %in% c("point","jitter")) {
point_args <- .get_point_args(colour_by,
shape_by = shape_by,
size_by = size_by,
alpha = point_alpha,
shape = point_shape,
size = point_size,
colour = point_colour)
point_args$args$mapping$y <- sym("Y")
if (layout == "point"){
plot_out <- plot_out +
do.call(geom_density, geom_args$args) +
do.call(facet_grid, grid_args)

shape_by <- NULL
size_by <- NULL
angle_x_text <- FALSE
} else if (layout %in% c("point", "jitter", "box", "violin")) {
if (layout == "point") {
plot_out <- plot_out + do.call(geom_point, geom_args$args)
} else if (layout == "jitter") {
geom_args$args$height <- 0.25
plot_out <- plot_out + do.call(geom_jitter, geom_args$args)
} else if (layout == "box") {
plot_out <- plot_out + do.call(geom_boxplot, geom_args$args)
} else if (layout == "violin") {
plot_out <- plot_out + do.call(geom_violin, geom_args$args)
}
do.call(geom_point, point_args$args)
} else if (layout == "jitter") {
point_args$args$height <- 0.25
plot_out <- plot_out +
do.call(geom_jitter, point_args$args)
} else {
stop(".")
}
} else{
stop("Unsupported layout option: '",layout,"'.", call. = FALSE)
}

# If colour_by is specified, colours are resolved
if (!is.null(colour_by)) {
plot_out <- .resolve_plot_colours(plot_out, density_data$colour_by, colour_by, fill = geom_args$fill, na.translate = FALSE)
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