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[Hotfix]: issue with plots when both model and grouping are present #196

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Merged
Schiano-NOAA merged 3 commits into from
Feb 27, 2026
Merged

[Hotfix]: issue with plots when both model and grouping are present #196

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10a1f2c
add interaction to timeseries plot line
Schiano-NOAA Feb 25, 2026
1fa996c
remove duplicated plot_timeseries
Schiano-NOAA Feb 25, 2026
da2f2c0
update documentation for plot timeseries
Schiano-NOAA Feb 26, 2026
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210 changes: 22 additions & 188 deletions R/utils_plot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ plot_timeseries <- function(
x = .data[[x]],
ymin = estimate_lower,
ymax = estimate_upper,
fill = group_var
fill = interaction(model, group_var)
),
alpha = 0.3
) +
Expand All @@ -99,9 +99,9 @@ plot_timeseries <- function(
ggplot2::aes(
x = .data[[x]],
y = .data[[y]],
linetype = group_var,
# linetype = group_var,
# linetype = ifelse(!is.null(group), group_var, "solid"),
color = model
color = interaction(model, group_var)
),
# linewidth = 1.0,
...
Expand All @@ -122,195 +122,29 @@ plot_timeseries <- function(
)

# Add labels to axis and legend
labs <- plot + ggplot2::labs(
x = xlab,
y = ylab,
color = "Model",
linetype = cap_first_letter(group),
fill = cap_first_letter(group),
shape = cap_first_letter(group)
)

# Remove linetype or point when there is no grouping
if (is.null(group) & length(unique(dat$model)) == 1) {
labs <- switch(geom,
"line" = labs + ggplot2::guides(linetype = "none"),
"point" = labs + ggplot2::guides(shape = "none"),
# return plot if option beyond line and point for now
labs
)
}
if (length(unique(dat$model)) == 1) {
labs <- switch(geom,
"line" = labs + ggplot2::guides(color = "none"),
"point" = labs + ggplot2::guides(color = "none"),
"area" = labs + ggplot2::guides(fill = "none"),
# return plot if option beyond line and point for now
labs
)
}

# Calc axis breaks
x_n_breaks <- axis_breaks(dat[[x]])
breaks <- ggplot2::scale_x_continuous(
breaks = x_n_breaks,
guide = ggplot2::guide_axis(
minor.ticks = TRUE
)
)

# Put together final plot
final <- labs + breaks + ggplot2::expand_limits(y = 0) +
ggplot2::scale_y_continuous(
labels = scales::label_comma()
if (length(unique(dat$model)) > 1 & !is.null(group)) {
labs <- plot + ggplot2::labs(
x = xlab,
y = ylab
# color = "Model",
# linetype = cap_first_letter(group),
# fill = cap_first_letter(group),
# shape = cap_first_letter(group)
) +
ggplot2::theme(legend.title = ggplot2::element_blank())
} else {
labs <- plot + ggplot2::labs(
x = xlab,
y = ylab,
color = "Model",
linetype = cap_first_letter(group),
fill = cap_first_letter(group),
shape = cap_first_letter(group)
)

# Remove legend if no group is selected
if (is.null(group) & is.data.frame(dat) & any(is.na(unique(dat$model)))) {
final <- final + ggplot2::theme(legend.position = "none")
}

# Check if facet(s) are desired
if (!is.null(facet)) {
facet <- paste("~", paste(facet, collapse = " + "))
facet_formula <- stats::reformulate(facet)

final <- final + ggplot2::facet_wrap(facet_formula)
}
final
}

#------------------------------------------------------------------------------

#' Create plot with error
#'
#' @param dat filtered data frame from standard output file(s) preformatted for
#' the target label from \link[stockplotr]{filter_data}
#' @param x a string of the column name of data used to plot on the x-axis (default
#' is "year")
#' @param y a string of the column name of data used to plot on the y-axis (default
#' is "estimate")
#' @param geom type of geom to use for plotting found in ggplot2 (e.g. "point",
#' "line", etc.). Default is "line". Other options are "point" and "area".
#' @param xlab a string of the x-axis label (default is "Year")
#' @param ylab a string of the y-axis label. If NULL, it will be set to the name
#' of `y`.
#' @param group a string of a single column that groups the data (e.g. "fleet",
#' "sex", "area", etc.). Currently can only have one level of grouping.
#' @param facet a string or vector of strings of a column that facets the data
#' (e.g. "year", "area", etc.)
#' @param ... inherited arguments from internal functions from ggplot2::geom_xx
#'
#'
#' @returns Create a time series plot for a stock assessment report. The user
#' has options to create a line, point, or area plot where the x-axis is year
#' and Y can vary for any time series quantity. Currently, grouping is
#' restricted to one group where faceting can be any number of facets.
#' @export
#'
#' @examples
#' \dontrun{
#' plot_timeseries(dat,
#' x = "year",
#' y = "estimate",
#' geom = "line",
#' xlab = "Year",
#' ylab = "Biomass",
#' group = "fleet",
#' facet = "area"
#' )
#' }
plot_timeseries <- function(
dat,
x = "year",
y = "estimate",
geom = "line",
xlab = "Year",
ylab = NULL,
group = NULL,
facet = NULL,
...
) {
# Start plot
plot <- ggplot2::ggplot()
# make into new geom?
# more defaults and fxnality for ggplot

# Add geom
plot <- switch(geom,
"point" = {
point_size <- ifelse(
is.null(list(...)$size),
2.0,
list(...)$size
)
plot +
ggplot2::geom_point(
data = dat,
ggplot2::aes(
.data[[x]],
.data[[y]],
# TODO: add more groupings
# shape = ifelse(any(grepl("shape", names(group))), .data[[group[[grep("shape", names(group))]]]], 1),
# color = ifelse(any(grepl("color", names(group))), .data[[group[[grep("color", names(group))]]]], "black")
color = model,
shape = group_var
),
# size = point_size,
...
)
},
"line" = {
plot +
ggplot2::geom_ribbon(
dat = dat |> dplyr::filter(!is.na(estimate_lower)),
ggplot2::aes(
x = .data[[x]],
ymin = estimate_lower,
ymax = estimate_upper
),
colour = "grey",
alpha = 0.3
) +
ggplot2::geom_line(
data = dat,
ggplot2::aes(
.data[[x]],
.data[[y]],
linetype = group_var,
# linetype = ifelse(!is.null(group), group_var, "solid"),
color = model
),
# linewidth = 1.0,
...
)
},
"area" = {
plot +
ggplot2::geom_area(
data = dat,
ggplot2::aes(
x = .data[[x]],
y = .data[[y]],
fill = model
),
...
)
}
)

# Add labels to axis and legend
labs <- plot + ggplot2::labs(
x = xlab,
y = ylab,
color = "Model",
linetype = cap_first_letter(group),
fill = cap_first_letter(group),
shape = cap_first_letter(group)
)

# Remove linetype or point when there is no grouping
if (is.null(group)) {
if (is.null(group) & length(unique(dat$model)) == 1) {
labs <- switch(geom,
"line" = labs + ggplot2::guides(linetype = "none"),
"point" = labs + ggplot2::guides(shape = "none"),
Expand Down
30 changes: 0 additions & 30 deletions man/plot_timeseries.Rd
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