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[feat]: enable user to add a reference line to the plot for each input dat #315

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[feat]: enable user to add a reference line to the plot for each input dat #315

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e912c0a
add note for where editing will occur
Schiano-NOAA Jul 21, 2026
c7acf3a
update reference_line to use plus operator and remove calc ref point …
Schiano-NOAA Jul 23, 2026
12348bc
add ifelse statement for single model ref line label
Schiano-NOAA Jul 24, 2026
ed04eef
other adjustments to allow the use to make ref explicit or search for…
Schiano-NOAA Jul 24, 2026
7b6170d
update ref line fxn man
Schiano-NOAA Jul 24, 2026
711627c
make adjustment to reference lines for plot_biomass
Schiano-NOAA Jul 24, 2026
98286c2
add new ref line approach for plot F
Schiano-NOAA Jul 24, 2026
6cb15b4
move reference line code into own function for simplicity
Schiano-NOAA Jul 27, 2026
b47e247
add new ref line function into other relevant fxns and replace code
Schiano-NOAA Jul 27, 2026
1ac2b74
remove lbs from B and F plots in ref line; consolidate note in utils
Schiano-NOAA Jul 28, 2026
222f420
add todo to adjust color of unfished ref pt
Schiano-NOAA Jul 28, 2026
1f44495
add missing pkg dependencies from used functions
Schiano-NOAA Jul 29, 2026
0ba22c4
set legends to show under certain conditions for elements of line plo…
Schiano-NOAA Jul 29, 2026
64b6e7b
comment out conditional removal of legend
Schiano-NOAA Jul 30, 2026
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31 changes: 6 additions & 25 deletions R/plot_biomass.R
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Original file line number Diff line number Diff line change
Expand Up @@ -141,37 +141,18 @@ plot_biomass <- function(
...
)
# Add reference line
# getting data set - an ifelse statement in the fxn wasn't working
if (relative) {
# don't add any reference line here and just add theme for final plot
final <- plt + theme_noaa()
} else {
if ("unfished" %in% c(names(ref_line), ref_line)) {
# find the minimum x axis value from the plot
min_year <- min <- ggplot2::ggplot_build(plt)[["data"]][[2]] |>
as.data.frame() |>
dplyr::pull(x) |>
min() |>
round(digits = 2)
# find the reference point value for unfished
ref_point <- calculate_reference_point(
dat = stockplotr::example_data,
reference_name = "biomass_unfished"
) / scale_amount
# add point to plot and add theme
final <- plt +
ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
theme_noaa()
} else {
final <- reference_line(
plot = plt,
dat = rp_dat,
label_name = "biomass",
reference = ref_line,
final <- plt +

@sbreitbart-NOAA sbreitbart-NOAA Jul 30, 2026

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I like the messages shown when a ref line isn't found. Here, it shows up for one model but not both, even though zero ref lines are shown (i.e., no message warning about a lack of ref line for the stockplotr example data, but it's not shown):

plot_biomass(dat = list("petrale" = dat, "skate" = skate), module = "TIME_SERIES")
! biomass_msy not found for skate
Warning messages:
1: Removed 1 row containing missing values or values
outside the scale range (geom_hline()).
2: Removed 1 row containing missing values or values
outside the scale range (geom_text()).

Image

add_reference_line(
dat = dat,
ref_line = ref_line,
label = "biomass",
scale_amount = scale_amount
) +
theme_noaa()
}
theme_noaa()
}

### Make RDA ----
Expand Down
21 changes: 13 additions & 8 deletions R/plot_fishing_mortality.R
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Original file line number Diff line number Diff line change
Expand Up @@ -76,14 +76,19 @@ plot_fishing_mortality <- function(
facet = facet,
...
)
# Add reference line and theme
final <- reference_line(
plot = plt,
dat = dat,
label_name = "fishing_mortality",
reference = ref_line,
scale_amount = 1
) + theme_noaa()
# Add reference line

@sbreitbart-NOAA sbreitbart-NOAA Jul 30, 2026

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I think this information should be added to the ref_line documentation so that people know what to expect when adding multiple reference lines. Adding an example with multiple models and reference lines would help clarify these rules too, as would adding a section to the FAQs about how to add reference lines in a few different situations

# Conditions for ref line
# 1. all are comparing same value = msy, target, unfished...
# 2. custom input vector = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
# 3. input vector of labels = c("msy", "target")
# getting data set - an ifelse statement in the fxn wasn't working
Comment on lines +80 to +84

@sbreitbart-NOAA sbreitbart-NOAA Jul 30, 2026

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Suggested change
# Conditions for ref line
# 1. all are comparing same value = msy, target, unfished...
# 2. custom input vector = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
# 3. input vector of labels = c("msy", "target")
# getting data set - an ifelse statement in the fxn wasn't working

(this is repeated in utils_plot.R)

final <- plt +
add_reference_line(
dat = dat,
ref_line = ref_line,
label = "fishing_mortality"
) +
theme_noaa()

### Make RDA ----
if (make_rda) {
Expand Down
42 changes: 9 additions & 33 deletions R/plot_spawning_biomass.R
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Original file line number Diff line number Diff line change
Expand Up @@ -145,12 +145,6 @@ plot_spawning_biomass <- function(
)
}
)
# Pull first df if in a list to find reference point
if (!is.data.frame(dat)) {
rp_dat <- dat[[1]]
} else {
rp_dat <- dat
}

if (relative & scale_amount > 1) {
cli::cli_alert_warning("Scale amount is not applicable when relative = TRUE. Resetting scale_amount to 1.")
Expand Down Expand Up @@ -202,41 +196,23 @@ plot_spawning_biomass <- function(
ylab = spawning_biomass_label,
group = group,
# add check in case facet is returned as character(0)
facet = if (length(facet) > 0) facet else NULL,
...
facet = if (length(facet) > 0) facet else NULL#,

@sbreitbart-NOAA sbreitbart-NOAA Jul 30, 2026

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Are the comments leftover from testing?

# ...
)
# Add reference line
# getting data set - an ifelse statement in the fxn wasn't working
if (relative) {
# don't add any reference line here and just add theme for final plot
final <- plt + theme_noaa()
} else {
if ("unfished" %in% c(names(ref_line), ref_line)) {
# find the minimum x axis value from the plot
min_year <- min <- ggplot2::ggplot_build(plt)[["data"]][[2]] |>
as.data.frame() |>
dplyr::pull(x) |>
min() |>
round(digits = 2)
# find the reference point value for unfished
ref_point <- calculate_reference_point(
dat = rp_dat,
reference_name = "spawing_biomass_unfished"
) / scale_amount
# add point to plot and add theme
final <- plt +
ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
theme_noaa()
} else {
final <- reference_line(
plot = plt,
dat = rp_dat,
final <- plt +
add_reference_line(
dat = dat,
ref_line = ref_line,
label = "spawning_biomass",
lbs = lbs,
label_name = "spawning_biomass",
reference = ref_line,
scale_amount = scale_amount
) + theme_noaa()
}
) +
theme_noaa()
}

### Make RDA ----
Expand Down
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