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Carbon tracking tab updated
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Plots generating smoothly, conditional formatting so both show at the top of the page
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@ciara-donegan
ciara-donegan committed Jan 16, 2024
1 parent 2243b56 commit 8a2d40f
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Showing 2 changed files with 104 additions and 45 deletions.
144 changes: 103 additions & 41 deletions h2/components/modules/mod_tracking.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,12 @@ tracking_ui <- function(id) {
"SSP 5-8.5"="input/hector_ssp585.ini"),
selected = "input/hector_ssp245.ini", inline=TRUE,
shape = "square", width = "80%"),
bsPopover(ns("ssp_path"), title="",content="Select a Shared Socioeconomic Pathway to plot.",
placement = "top", trigger = "hover", options = NULL),

sliderInput(ns("start"), label="Select year to begin tracking:",
min = 1750, max = 2200, value = 1900, sep="",step=5),

selectInput(ns("pool"), label="Select pool to view:",
choices = list("High latitude ocean"="HL Ocean",
"Low latitude ocean"="LL Ocean",
Expand All @@ -26,29 +30,53 @@ tracking_ui <- function(id) {
"Detritus"="Detritus",
"Soil"="Soil"),
selected="Atmosphere"),
radioButtons(ns("view"), label="View:",
choices = list("Carbon Amount"=1,
"Carbon Fraction"=2),
selected = 1),
radioButtons(ns("ff"), label="Toggle fossil fuels:",
choices = list("On"=1,"Off"=2)),
radioButtons(ns("plotSelect"), label="Select plot to view:",

prettyRadioButtons(ns("plotSelect"), label="Select plot to view:",
choices = list("Area Plot"=1,
"Animated Bar Plot (Carbon Amount Only)"=2),
"Animated Bar Plot"=2),
selected=1),

prettyRadioButtons(ns("ff"), label="Toggle fossil fuels:",
choices = list("On"=1,"Off"=2)),
bsPopover(ns("ff"), title="",content="Select whether you want fossil fuels to be included (On), or only non-anthropogenic sources of carbon (Off).",
placement = "top", trigger = "hover", options = NULL),

conditionalPanel(
condition = "input.plotSelect == 1",
prettyRadioButtons(ns("view"), label="View:",
choices = list("Carbon Amount"=10,
"Carbon Fraction"=7),
selected = 10),
bsPopover(ns("view"), title="",content="Select whether you want to view the total amounts of carbon in each pool (Carbon Amount), or the fraction each pool has of the total amount in the system (Carbon Fraction).",
placement = "top", trigger = "hover", options = NULL),
ns = NS("tracking_1")
),
actionButton(ns("generate"),"Generate"),
downloadButton(ns("downloadGif"),"Download Plot"),
),
mainPanel(
withSpinner(plotlyOutput(ns("fig")),type=7)
conditionalPanel(
condition = "input.plotSelect == 1",
withSpinner(plotlyOutput(ns("fig"))),
ns = NS("tracking_1")
),
conditionalPanel(
condition = "input.plotSelect == 2",
withSpinner(imageOutput(ns("gif"))),
ns = NS("tracking_1")
)
)
)
}

tracking_server <- function(id) {
moduleServer(id, function(input, output, session) {

# Get shinycssloaders to not appear until plots are generated
#output$fig <- renderPlotly(NULL)
#output$gif <- renderImage(NULL)

observe({
#browser()
# Run Hector w/ carbon tracking
ini_file <- reactive({system.file(input$ssp_path,package="hector")})
core <- newcore(ini_file())
Expand All @@ -59,7 +87,7 @@ tracking_server <- function(id) {
run(core, runtodate = 2300)
print("Gathering data...")
df <- get_tracking_data(core)

# clean up pool names
df[df=="atmos_co2"] <- "Atmosphere"
df[df=="deep"] <- "Deep Ocean"
Expand All @@ -82,9 +110,11 @@ tracking_server <- function(id) {
df <- subset(df, source_name!="permafrost_c")
df <- subset(df, source_name!="thawedp_c")

# bar width for area plot
#barwidth <- reactive({(2100-input$start)/50})
#browser()
# fill in any missing pools
df <- df[order(df$source_name),] # sort by source, then year, so sources are always in same order each year
df <- df[order(df$year),]


# rank column for moving bar plot
df <- df %>%
group_by(year) %>%
Expand All @@ -95,20 +125,22 @@ tracking_server <- function(id) {
frac_lbl = paste0(format(round(source_fraction,2),nsmall=2))) %>%
group_by(source_name) %>%
ungroup()

#browser()

# Plotting
plotSelect <- reactive({input$plotSelect})
plotSelect <- reactive({input$plotSelect}) # area or bar
view <- reactive({input$view}) # fraction or amount
view <- as.numeric(view())
#browser()

# Area plot
if (plotSelect() == 1) {

print("Generating plot...")
area_plot <-
plot_ly(
filter(df, source_name == "HL Ocean"),
x = ~ year,
y = ~ source_amt,
y = ~ source_amt,
name = "HL Ocean",
type = "scatter",
mode = "none",
Expand All @@ -118,56 +150,56 @@ tracking_server <- function(id) {
area_plot <-
area_plot %>% add_trace(
data = filter(df, source_name == "LL Ocean"),
y = ~ source_amt,
y = ~ source_amt,
name = "LL Ocean",
fillcolor = "#3B528BFF"
)
area_plot <-
area_plot %>% add_trace(
data = filter(df, source_name == "Intermediate Ocean"),
y = ~ source_amt,
y = ~ source_amt,
name = "Intermediate Ocean",
fillcolor = "#472D7BFF"
)
area_plot <-
area_plot %>% add_trace(
data = filter(df, source_name == "Deep Ocean"),
y = ~ source_amt,
y = ~ source_amt,
name = "Deep Ocean",
fillcolor = "#440154FF"
)
area_plot <-
area_plot %>% add_trace(
data = filter(df, source_name == "Atmosphere"),
y = ~ source_amt,
y = ~ source_amt,
name = "Atmosphere",
fillcolor = "#21908CFF"
)
area_plot <-
area_plot %>% add_trace(
data = filter(df, source_name == "Vegetation"),
y = ~ source_amt,
y = ~ source_amt,
name = "Vegetation",
fillcolor = "#27AD81FF"
)
area_plot <-
area_plot %>% add_trace(
data = filter(df, source_name == "Soil"),
y = ~ source_amt,
y = ~ source_amt,
name = "Soil",
fillcolor = "#5DC863FF"
)
area_plot <-
area_plot %>% add_trace(
data = filter(df, source_name == "Detritus"),
y = ~ source_amt,
y = ~ source_amt,
name = "Detritus",
fillcolor = "#AADC32FF"
)
area_plot <-
area_plot %>% add_trace(
data = filter(df, source_name == "Fossil Fuels"),
y = ~ source_amt,
y = ~ source_amt,
name = "Fossil Fuels",
fillcolor = "#FDE725FF"
)
Expand All @@ -179,24 +211,54 @@ tracking_server <- function(id) {
output$fig <- renderPlotly(area_plot)

} else if (plotSelect() == 2) {

bar_plot <-
plot_ly(
df,
y = ~ source_name,
x = ~ source_amt,
type = "bar",
orientation = "h",
frame = ~ year
#color = ~ source_name
)

output$fig <- renderPlotly(bar_plot)

output$gif <- renderImage({
# Temp file to save output
outfile <- tempfile(fileext='.gif')

# Make animation
p <- ggplot(df,aes(fill=source_name,color=source_name,
x=reorder(source_name,source_amt),
y=source_amt)) +
geom_bar(stat="identity") +
geom_text(aes(y=0, label = paste(source_name, " ")),
vjust = 0.2, hjust = 1, size = 6) +
geom_text(aes(y = source_amt, label = paste(" ",amt_lbl), hjust=0),
size = 6) +
coord_flip(clip = "off", expand = FALSE) +
theme_void() +
theme(plot.title = element_text(size=20,face="bold"),
plot.subtitle = element_text(size=18),
legend.position="none",
panel.grid.major.x = element_line(size=.1,color="snow2"),
panel.grid.minor.x = element_line(size=.1,color="snow2"),
plot.margin = margin(1,6,1,6,"cm")) +
ylab("Carbon (Pg)") +
xlab("") +
scale_fill_viridis_d() +
scale_color_viridis_d() +

# gganimate
transition_time(year) +
ease_aes('linear')

# Animate
anim <- p + transition_states(year,transition_length=4,
state_length=2,wrap=FALSE) +
view_follow(fixed_x = TRUE) +
labs(title=paste0(selectedPool()," Carbon Sources"),
subtitle="Year: {closest_state}")

anim_save("outfile.gif", animate(anim, height = 500, width = 800,
end_pause=30))
list(src = 'outfile.gif',
contentType = 'image/gif'
# width = 800,
# height = 300,
# alt = "An animation tracking the sources of carbon in a chosen pool"
)}, deleteFile = TRUE)
}



}) %>%
bindEvent(input$generate)
})
Expand Down
5 changes: 1 addition & 4 deletions h2/global.r
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,12 +5,11 @@ library(dplyr)
library(ggplot2)
library(shinycssloaders)
library(plotly)
library(shinyalert) # don't need if we have shinyWidgets?
library(DT)
library(shinyWidgets)
library(gganimate)
library(gifski)
library(tidyverse)
library(shinyBS)

#setwd("~/GitHub/hectorui/h2")

Expand Down Expand Up @@ -40,13 +39,11 @@ HectorInputs <- R6Class(
package = "hector")) {
self$ini_file <- ini_file
self$time <- time
# self$time[2] <- time
self$output <- list()
self$no_save <- NULL
self$run_name <- 1
self$inputs <- list()
self$selected_var <- "CO2_concentration"
#stopifnot(time[2] > time[1]) #gotta have the start year before the end year
}
)
)
Expand Down

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