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plot_module.R
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plot_module.R
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# Pick plot axes ----------------------------------------------------------
axis_picker <- function(input_axis, input_model) {
switch(input_axis,
"206Pb/204Pb" = list(input_axis, "<sup>206</sup>Pb/<sup>204</sup>Pb", expression(""^"206"*"Pb/"^"204"*"Pb")),
"207Pb/204Pb" = list(input_axis, "<sup>207</sup>Pb/<sup>204</sup>Pb", expression(""^"207"*"Pb/"^"204"*"Pb")),
"208Pb/204Pb" = list(input_axis, "<sup>208</sup>Pb/<sup>204</sup>Pb", expression(""^"208"*"Pb/"^"204"*"Pb")),
"206Pb/207Pb" = list(input_axis, "<sup>206</sup>Pb/<sup>207</sup>Pb", expression(""^"206"*"Pb/"^"207"*"Pb")),
"208Pb/207Pb" = list(input_axis, "<sup>208</sup>Pb/<sup>207</sup>Pb", expression(""^"208"*"Pb/"^"207"*"Pb")),
"204Pb/206Pb" = list(input_axis, "<sup>204</sup>Pb/<sup>206</sup>Pb", expression(""^"204"*"Pb/"^"206"*"Pb")),
"207Pb/206Pb" = list(input_axis, "<sup>207</sup>Pb/<sup>206</sup>Pb", expression(""^"207"*"Pb/"^"206"*"Pb")),
"208Pb/206Pb" = list(input_axis, "<sup>208</sup>Pb/<sup>206</sup>Pb", expression(""^"208"*"Pb/"^"206"*"Pb")),
"Model Age" = switch(input_model,
"Stacey & Kramers 1975" = list("Model_Age_SK75", "Model Age<sub>Stacey & Kramers 1975</sub> [Ma]", expression("Model Age"["Stacey & Kramers 1975"]*" [Ma]")),
"Cumming & Richards 1975" = list("Model_Age_CR75", "Model Age<sub>Cumming & Richards 1975</sub> [Ma]", expression("Model Age"["Cumming & Richards 1975"]*" [Ma]")),
"Albarede & Juteau 1984" = list("Model_Age_AJ84", "Model Age<sub>Albarède & Juteau 1984</sub> [Ma]", expression("Model Age"["Albarede & Juteau 1984"]*" [Ma]")),
"Albarede et al. 2012" = list("Model_Age_ADB12", "Model Age<sub>Albarède et al. 2012</sub> [Ma]", expression("Model Age"["Albarède et al. 2012"]*" [Ma]"))
),
"mu" = switch(input_model,
"Stacey & Kramers 1975" = list("mu_SK75", "\u03BC<sub>Stacey & Kramers 1975</sub>", expression(mu["Stacey & Kramers 1975"])),
"Cumming & Richards 1975" = list("mu_CR75", "\u03BC<sub>Cumming & Richards 1975</sub>", expression(mu["Cumming & Richards 1975"])),
"Albarede & Juteau 1984" = list("mu_AJ84", "\u03BC<sub>Albarede & Juteau 1984</sub>", expression(mu["Albarede & Juteau 1984"])),
"Albarede et al. 2012" = list("mu_ADB12", "\u03BC<sub>Albarède et al. 2012</sub>", expression(mu["Albarède et al. 2012"]))
),
"kappa" = switch(input_model,
"Stacey & Kramers 1975" = list("kappa_SK75", "\u03BA<sub>Stacey & Kramers 1975</sub>", expression(kappa["Stacey & Kramers 1975"])),
"Cumming & Richards 1975" = list("kappa_CR75", "\u03BA<sub>Cumming & Richards 1975</sub>", expression(kappa["Cumming & Richards 1975"])),
"Albarede & Juteau 1984" = list("kappa_AJ84", "\u03BA<sub>Albarede & Juteau 1984</sub>", expression(kappa["Albarede & Juteau 1984"])),
"Albarede et al. 2012" = list("kappa_ADB12", "\u03BA<sub>Albarède et al. 2012</sub>", expression(kappa["Albarède et al. 2012"]))
)
)
}
# Pick palette ------------------------------------------------------------
palette_picker <- function(input_palette, input_style) {
if (!input_style %in% c("2D Scatter")) { # discrete scales
if (input_palette %in% c("viridis", "magma", "inferno", "plasma", "cividis")) {
palette <- list(scale_color_viridis_d(option = input_palette), scale_fill_viridis_d(option = input_palette))
}
if (input_palette %in% c("Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples", "RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd")) {
palette <- list(scale_color_brewer(palette = input_palette, type = "seq"), scale_fill_brewer(palette = input_palette, type = "seq"))
}
if (input_palette %in% c("BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral")) {
palette <- list(scale_color_brewer(palette = input_palette, type = "div"), scale_fill_brewer(palette = input_palette, type = "div"))
}
if (input_palette %in% c("Accent", "Dark2", "Paired", "Pastel1", "Pastel2", "Set1", "Set2", "Set3")) {
palette <- list(scale_color_brewer(palette = input_palette, type = "qual"), scale_fill_brewer(palette = input_palette, type = "qual"))
}
} else { # continuous scales
if (input_palette %in% c("viridis", "magma", "inferno", "plasma", "cividis")) {
palette <- list(scale_color_viridis_c(option = input_palette), scale_fill_viridis_c(option = input_palette))
}
if (input_palette %in% c("Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples", "RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd")) {
palette <- list(scale_color_distiller(palette = input_palette, type = "seq"), scale_color_distiller(palette = input_palette, type = "seq"))
}
if (input_palette %in% c("BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral")) {
palette <- list(scale_color_distiller(palette = input_palette, type = "div"), scale_color_distiller(palette = input_palette, type = "div"))
}
if (input_palette %in% c("Accent", "Dark2", "Paired", "Pastel1", "Pastel2", "Set1", "Set2", "Set3")) {
palette <- list(scale_color_distiller(palette = input_palette, type = "qual"), scale_color_distiller(palette = input_palette, type = "qual"))
}
}
palette
}
# Plot ShinyModule --------------------------------------------------------------
plotExploreUI <- function(id, title_plot, start_y) {
ns <- NS(id)
tagList(
fluidRow(
tabBox(
id = "setting",
title = title_plot,
width = 6,
side = "right",
maximizable = TRUE,
tabPanel(
title = "Settings",
fluidRow(
column(
width = 4,
h5("Variables"),
selectizeInput(ns("x"), "X-axis", choices = c("206Pb/204Pb", "207Pb/204Pb", "208Pb/204Pb", "206Pb/207Pb", "208Pb/207Pb", "204Pb/206Pb", "207Pb/206Pb", "208Pb/206Pb", "Model Age", "mu", "kappa"),
selected = "206Pb/204Pb"),
selectizeInput(ns("y"), "Y-axis", choices = c("none", "206Pb/204Pb", "207Pb/204Pb", "208Pb/204Pb", "206Pb/207Pb", "208Pb/207Pb", "204Pb/206Pb", "207Pb/206Pb", "208Pb/206Pb", "Model Age", "mu", "kappa"),
selected = start_y),
selectizeInput(ns("z"), "Z-axis or fill", choices = c("none", "206Pb/204Pb", "207Pb/204Pb", "208Pb/204Pb", "206Pb/207Pb", "208Pb/207Pb", "204Pb/206Pb", "207Pb/206Pb", "208Pb/206Pb", "Model Age", "mu", "kappa"),
selected = "none"),
selectizeInput(ns("model"), "Age model", choices = c("Stacey & Kramers 1975", "Cumming & Richards 1975", "Albarede & Juteau 1984", "Albarede et al. 2012"),
options = list(placeholder = 'Please select the age model.'), selected = "Stacey & Kramers 1975"),
),
column(
width = 4,
h5("Style"),
selectInput(ns("style"), "Plot style", choices = c("Point", "Density 2D", "Point + Density 2D"), selected = "Point"),
uiOutput(ns("add1")),
uiOutput(ns("add2")),
uiOutput(ns("add3"))
),
column(
width = 4,
h5("Design"),
sliderInput(ns("alpha"), label = "Transparency", value = 0.5, min = 0, max = 1),
sliderInput(ns("size_reference"), label = "Point size or linewidth", value = 1, min = 0, max = 10, step = .1),
sliderInput(ns("size_upload"), label = "Size of uploaded data", value = 2, min = 0, max = 10, step = .1)
)
)
),
tabPanel(
title = "Data Viewer",
DT::dataTableOutput(ns("plot_data"))
)
),
tabBox(
id = "Plots",
title = paste0("View ", tolower(title_plot)),
width = 6,
side = "right",
maximizable = TRUE,
tabPanel(
title = "Interactive",
plotlyOutput(ns("plot_interactive"))
),
tabPanel(
title = "Print preview",
plotOutput(ns("plot_print"))
)
)
)
)
}
plotExploreServer <- function(id, data_reference, data_custom, group_ref, input_palette) {
moduleServer(
id,
function(input, output, session) {
ns <- session$ns
w <- Waiter$new(id = c(ns("plot_print"), ns("plot_interactive")))
plotModule_iv <- InputValidator$new()
plotModule_iv$add_rule("x", sv_in_set(c("206Pb/204Pb", "207Pb/204Pb", "208Pb/204Pb", "206Pb/207Pb", "208Pb/207Pb", "204Pb/206Pb", "207Pb/206Pb", "208Pb/206Pb", "Model Age", "mu", "kappa")))
plotModule_iv$add_rule("y", sv_in_set(c("none", "206Pb/204Pb", "207Pb/204Pb", "208Pb/204Pb", "206Pb/207Pb", "208Pb/207Pb", "204Pb/206Pb", "207Pb/206Pb", "208Pb/206Pb", "Model Age", "mu", "kappa")))
plotModule_iv$add_rule("z", sv_in_set(c("none", "206Pb/204Pb", "207Pb/204Pb", "208Pb/204Pb", "206Pb/207Pb", "208Pb/207Pb", "204Pb/206Pb", "207Pb/206Pb", "208Pb/206Pb", "Model Age", "mu", "kappa")))
plotModule_iv$add_rule("model", sv_in_set(c("Stacey & Kramers 1975", "Cumming & Richards 1975", "Albarede & Juteau 1984", "Albarede et al. 2012")))
plotModule_iv$add_rule("style", sv_in_set(c("2D Scatter", "3D Scatter", "Point", "Density 2D", "Point + Density 2D", "Density", "Density filled", "Histogram", "Frequency polygon", "Frequency polygon filled", "Boxplot")))
plotModule_iv$add_rule("alpha", sv_numeric())
plotModule_iv$add_rule("alpha", sv_between(0, 1))
plotModule_iv$add_rule("size_reference", sv_numeric())
plotModule_iv$add_rule("size_reference", sv_between(0, 10))
plotModule_iv$add_rule("size_upload", sv_numeric())
plotModule_iv$add_rule("size_upload", sv_between(0, 10))
plotModule_iv$add_rule("add_position", sv_optional())
plotModule_iv$add_rule("add_quantiles", sv_optional())
plotModule_iv$add_rule("add_minprob", sv_optional())
plotModule_iv$add_rule("add_bins", sv_optional())
plotModule_iv$add_rule("add_fill", sv_optional())
plotModule_iv$add_rule("add_quantiles", sv_optional())
plotModule_iv$add_rule("add_minprob", sv_optional())
plotModule_iv$add_rule("add_bins", sv_optional())
plotModule_iv$add_rule("add_position", sv_in_set(c("identity" , "stack", "fill")))
plotModule_iv$add_rule("add_quantiles", sv_integer())
plotModule_iv$add_rule("add_minprob", sv_numeric())
plotModule_iv$add_rule("add_bins", sv_integer())
plotModule_iv$add_rule("add_fill", ~ if(!is.logical(.)) "Do not hack the app.")
plotModule_iv$add_rule("add_quantiles", sv_between(1, 10))
plotModule_iv$add_rule("add_minprob", sv_between(0, 1))
plotModule_iv$add_rule("add_bins", sv_between(1, 100))
plotModule_iv$enable()
x <- reactive({ axis_picker(input$x, input$model) })
y <- reactive({ if (input$y == "none") {NULL} else {axis_picker(input$y, input$model)} })
z <- reactive({ if (input$z == "none" | input$y == "none") {NULL} else {axis_picker(input$z, input$model)} })
palette <- reactive({ palette_picker(input_palette(), input$style) })
observe({
plot_styles <- c("Density", "Density filled", "Histogram", "Frequency polygon", "Frequency polygon filled", "Boxplot") # , "Violin" - Bug with plotly
if (!is.null(y()) && is.null(z())) {plot_styles <- c("Point", "Density 2D", "Point + Density 2D")}
if (!is.null(y()) && !is.null(z())) {plot_styles <- c("2D Scatter", "3D Scatter")}
updateSelectInput(session, "style", choices = plot_styles, selected = plot_styles[1])
output$add1 <- renderUI({
req(input$style)
switch(input$style,
"Density" = selectInput(ns("add_position"), "Arrangement of groups", choices = c("Separate" = "identity" , "Stacked" = "stack", "Stacked & normalised" = "fill")),
"Density filled" = selectInput(ns("add_position"), "Arrangement of groups", choices = c("Separate" = "identity" , "Stacked" = "stack", "Stacked & normalised" = "fill")),
"Histogram" = selectInput(ns("add_position"), "Arrangement of groups", choices = c("Separate" = "identity" , "Stacked" = "stack", "Stacked & normalised" = "fill")),
"Frequency polygon" = selectInput(ns("add_position"), "Arrangement of groups", choices = c("Separate" = "identity" , "Stacked" = "stack", "Stacked & normalised" = "fill")),
"Frequency polygon filled" = selectInput(ns("add_position"), "Arrangement of groups", choices = c("Separate" = "identity" , "Stacked" = "stack", "Stacked & normalised" = "fill")),
#"Violin" = selectInput(ns("add_scale"), "Display method", choices = c("Uniform area" = "area", "Area scaled to counts" = "count", "Uniform maximum width" = "width")),
"Density 2D" = sliderInput(ns("add_quantiles"), label = "Number of quantiles", min = 1, max = 10, step = 1, value = 4),
"Point + Density 2D" = sliderInput(ns("add_quantiles"), label = "Number of quantiles", min = 1, max = 10, step = 1, value = 4),
NULL
)
})
output$add2 <- renderUI({
req(input$style)
switch(input$style,
#"Density" = selectInput(ns("add_afterstat"), "Method", choices = c("Density" = "density", "Density * count" = "count", "Normalised density" = "scaled")),
#"Density filled" = selectInput(ns("add_afterstat"), "Method", choices = c("Density" = "density", "Density * count" = "count", "Normalised density" = "scaled")),
#"Histogram" = selectInput(ns("add_afterstat"), "Method", choices = c("Count" = "count", "Density" = "density ", "Normalised count" = "ncount", "Normalised density" = "ndensity")),
#"Frequency polygon" = selectInput(ns("add_afterstat"), "Method", choices = c("Count" = "count", "Density" = "density ", "Normalised count" = "ncount", "Normalised density" = "ndensity")),
#"Frequency polygon filled" = selectInput(ns("add_afterstat"), "Method", choices = c("Count" = "count", "Density" = "density ", "Normalised count" = "ncount", "Normalised density" = "ndensity")),
"Density 2D" = sliderInput(ns("add_minprob"), label = "Smallest displayed quantile", min = 0, max = 1, step = 0.01, value = 0.02),
"Point + Density 2D" = sliderInput(ns("add_minprob"), label = "Smallest displayed quantile", min = 0, max = 1, step = 0.01, value = 0.02),
NULL
)
})
output$add3 <- renderUI({
req(input$style)
switch(input$style,
"Histogram" = sliderInput(ns("add_bins"), "Number of bins", value = 30, min = 1, max = 100, step = 1),
"Frequency polygon" = sliderInput(ns("add_bins"), "Number of bins", value = 30, min = 1, max = 100, step = 1),
"Frequency polygon filled" = sliderInput(ns("add_bins"), "Number of bins", value = 30, min = 1, max = 100, step = 1),
"Density 2D" = checkboxInput(ns("add_fill"), label = "Filled polygons"),
NULL
)
})
})
plot <- reactive({
w$show()
req(plotModule_iv$is_valid(), data_reference())
plot_build <- ggplot(data_reference()) +
palette() +
theme_bw() +
guides(alpha = "none", size = "none")
if (is.null(y()) && is.null(z())) {
# label_y <- {
# req(input$add_afterstat)
# switch (input$add_afterstat,
# "density" = "Density",
# "count" = if (input$style == "Density") {"n * density"} else {"Count"},
# "ndensity" = "normalised density",
# "ncount" = "normalised count"
# )
# }
switch(input$style,
"Density" = {
req(input$add_position) #input$add_afterstat,
plot_build <- plot_build +
stat_density(geom = "line", aes(x = .data[[x()[[1]]]], colour = .data[[group_ref()]], text = .data[[group_ref()]]),
position = input$add_position, alpha = input$alpha, size = input$size_reference) + # aes(y = after_stat(!!input$add_afterstat)),
labs(x = x()[[2]], y = "Density") #label_y)
if (!is.null(data_custom())) {
plot_build <- plot_build +
geom_density(data = data_custom(), aes(x = .data[[x()[[1]]]], linetype = group, text = group), size = input$size_upload, colour = "black") +
scale_linetype(name = if ("This study" %in% data_custom()$group) {NULL} else {"This study"})
}
},
"Density filled" = {
req(input$add_position) #input$add_afterstat,
plot_build <- plot_build +
geom_density(aes(x = .data[[x()[[1]]]], colour = .data[[group_ref()]], text = .data[[group_ref()]], fill = .data[[group_ref()]]),
position = input$add_position, alpha = input$alpha, size = input$size_reference) + # aes(y = after_stat(!!input$add_afterstat)),
labs(x = x()[[2]], y = "Density") #label_y)
if (!is.null(data_custom())) {
plot_build <- plot_build +
geom_density(data = data_custom(), aes(x = .data[[x()[[1]]]], linetype = group, text = group), size = input$size_upload, colour = "black") +
scale_linetype(name = if ("This study" %in% data_custom()$group) {NULL} else {"This study"})
}
},
"Histogram" = {
req(input$add_bins, input$add_position)# input$add_afterstat,
plot_build <- plot_build +
geom_histogram(aes(x = .data[[x()[[1]]]], colour = .data[[group_ref()]], text = .data[[group_ref()]], fill = .data[[group_ref()]]),
position = input$add_position, bins = input$add_bins, alpha = input$alpha, size = input$size_reference) + # aes(y = after_stat(!!input$add_afterstat)),
labs(x = x()[[2]], y = "Count") #label_y)
if (!is.null(data_custom())) {
plot_build <- plot_build +
geom_histogram(data = data_custom(), aes(x = .data[[x()[[1]]]], linetype = group, text = group), size = input$size_upload, alpha = .25, colour = "black") +
scale_linetype(name = if ("This study" %in% data_custom()$group) {NULL} else {"This study"})
}
},
"Frequency polygon" = {
req(input$add_bins, input$add_position) # input$add_afterstat,
plot_build <- plot_build +
geom_freqpoly(aes(x = .data[[x()[[1]]]], colour = .data[[group_ref()]], text = .data[[group_ref()]]),
position = input$add_position, bins = input$add_bins, alpha = input$alpha, size = input$size_reference) + # aes(y = after_stat(!!input$add_afterstat)),
labs(x = x()[[2]], y = "Count") #label_y)
if (!is.null(data_custom())) {
plot_build <- plot_build +
geom_freqpoly(data = data_custom(), aes(x = .data[[x()[[1]]]], linetype = group, text = group), size = input$size_upload, colour = "black") +
scale_linetype(name = if ("This study" %in% data_custom()$group) {NULL} else {"This study"})
}
},
"Frequency polygon filled" = {
req(input$add_bins, input$add_position) # input$add_afterstat,
plot_build <- plot_build +
geom_area(stat = "bin", aes(x = .data[[x()[[1]]]], colour = .data[[group_ref()]], text = .data[[group_ref()]], fill = .data[[group_ref()]]),
position = input$add_position, bins = input$add_bins, alpha = input$alpha, size = input$size_reference) + # aes(y = after_stat(!!input$add_afterstat)),
labs(x = x()[[2]], y = "Count") #label_y)
if (!is.null(data_custom())) {
plot_build <- plot_build +
geom_freqpoly(data = data_custom(), aes(x = .data[[x()[[1]]]], linetype = group, text = group), size = input$size_upload, colour = "black") +
scale_linetype(name = if ("This study" %in% data_custom()$group) {NULL} else {"This study"})
}
},
# "Violin" = {
# req(input$add_scale)
#
# plot_build <- plot_build +
# geom_violin(aes(y = .data[[x()[[1]]]], x = .data[[group_ref()]], text = .data[[group_ref()]]), draw_quantiles = input$add_quantiles, scale = input$add_scale, colour = "black", alpha = input$alpha, size = input$size_reference) +
# labs(y = x()[[2]], x = group_ref()) +
# theme(axis.text.x = element_text(angle = 45, hjust = 1))
#
# if (!is.null(data_custom())) {
# plot_build <- plot_build +
# geom_violin(data = data_custom(), aes(y = .data[[x()[[1]]]], x = group, text = group), fill = "grey50", size = input$size_upload, draw_quantiles = input$add_quantiles, scale = input$add_scale, colour = "black", size = input$size_upload) +
# scale_linetype(name = if ("This study" %in% data_custom()$group) {NULL} else {"This study"})
# }
# },
"Boxplot" = {
plot_build <- plot_build +
geom_boxplot(aes(y = .data[[x()[[1]]]], x = .data[[group_ref()]], text = .data[[group_ref()]]), colour = "black", alpha = input$alpha, size = input$size_reference) +
labs(y = x()[[2]], x = group_ref()) +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
if (!is.null(data_custom())) {
plot_build <- plot_build +
geom_boxplot(data = data_custom(), aes(y = .data[[x()[[1]]]], x = group, text = group),
fill = "grey50", size = input$size_upload, colour = "black") +
scale_linetype(name = if ("This study" %in% data_custom()$group) {NULL} else {"This study"})
}
}
)
}
if (!is.null(y()) && is.null(z())) {
switch(input$style,
"Point" = {
plot_build <- plot_build +
geom_point(aes(x = .data[[x()[[1]]]], y = .data[[y()[[1]]]], colour = .data[[group_ref()]], fill = .data[[group_ref()]], text = .data$tooltip),
size = input$size_reference, alpha = input$alpha) +
labs(x = x()[[2]], y = y()[[2]])
},
"Density 2D" = {
req(input$add_minprob, input$add_quantiles)
plot_build <- plot_build +
geom_kde2d(aes(x = .data[[x()[[1]]]], y = .data[[y()[[1]]]], group = .data[[group_ref()]], colour = .data[[group_ref()]],
fill = if (input$add_fill) {.data[[group_ref()]]} else {NA}, text = .data$tooltip),
size = input$size_reference, alpha = input$alpha, quantiles = input$add_quantiles, min_prob = input$add_minprob,
show.legend = if (input$add_fill) {c(colour = FALSE, fill = TRUE)} else {NA}) +
labs(x = x()[[2]], y = y()[[2]])
if (input$add_fill) { plot_build <- plot_build + guides(fill = guide_legend(title = group_ref())) }
},
"Point + Density 2D" = {
req(input$add_minprob, input$add_quantiles)
plot_build <- plot_build +
geom_point(aes(x = .data[[x()[[1]]]], y = .data[[y()[[1]]]], colour = .data[[group_ref()]], fill = .data[[group_ref()]], text = .data$tooltip),
size = input$size_reference) +
geom_kde2d(aes(x = .data[[x()[[1]]]], y = .data[[y()[[1]]]], group = .data[[group_ref()]], colour = .data[[group_ref()]], fill = .data[[group_ref()]], text = .data$tooltip),
size = input$size_reference/2, alpha = input$alpha, quantiles = input$add_quantiles, min_prob = input$add_minprob) +
labs(x = x()[[2]], y = y()[[2]])
}
)
if (!is.null(data_custom())) {
plot_build <- plot_build +
geom_point(data = data_custom(), aes(x = .data[[x()[[1]]]], y = .data[[y()[[1]]]], colour = .data[[group_ref()]], fill = .data[[group_ref()]], text = .data$tooltip, shape = group),
size = input$size_upload, colour = "black", fill = "black") +
scale_shape(name = if ("This study" %in% data_custom()$group) {NULL} else {"This study"})
}
}
if (!is.null(y()) && !is.null(z())) {
switch(input$style,
"2D Scatter" = {
plot_build <- plot_build +
geom_point(aes(x = .data[[x()[[1]]]], y = .data[[y()[[1]]]], color = .data[[z()[[1]]]], text = .data$tooltip),
size = input$size_reference, alpha = input$alpha) +
labs(x = x()[[2]], y = y()[[2]], color = z()[[2]])
if (!is.null(data_custom())) {
plot_build <- plot_build +
labs(x = x()[[2]], y = y()[[2]]) +
geom_point(data = data_custom(), aes(x = .data[[x()[[1]]]], y = .data[[y()[[1]]]], color = .data[[z()[[1]]]], text = .data$tooltip, shape = group),
size = input$size_upload, colour = "black", fill = "black") +
scale_shape(name = if ("This study" %in% data_custom()$group) {NULL} else {"This study"})
}
},
"3D Scatter" = {
if (input_palette() %in% c("viridis", "magma", "inferno", "plasma", "cividis")) {
palette_plotly <- viridis(option = input_palette(), n = length(unique(data_reference()[[group_ref()]])))
} else {
palette_plotly <- brewer.pal(length(unique(data_reference()[[group_ref()]])), name = input_palette())
}
plot_build <- plot_ly(type="scatter3d", mode = "markers", hovertemplate = "%{text}<extra></extra>", colors = palette_plotly) %>%
add_markers(data = data_reference(), x = ~.data[[x()[[1]]]], y = ~.data[[y()[[1]]]], z = ~.data[[z()[[1]]]], text = ~.data$tooltip, color= ~.data[[group_ref()]], alpha = input$alpha, size = I(input$size_reference*50)) %>%
layout(scene = list(xaxis = list(title = x()[[2]]),
yaxis = list(title = y()[[2]]),
zaxis = list(title = z()[[2]])
)
)
if (!is.null(data_custom())) {
plot_build <- plot_build %>%
add_markers(data = data_custom(), x = ~.data[[x()[[1]]]], y = ~.data[[y()[[1]]]], z = ~.data[[z()[[1]]]], text = ~.data$tooltip, alpha = 1, color= I("black"), size = I(input$size_custom), symbol = ~group)
}
}
)
}
plot_build
})
output$plot_interactive <- renderPlotly({
req(plot())
if (input$style != "Density 2D") {
plot_plotly <- ggplotly(p = plot(), tooltip = "text", dynamicTicks = TRUE, source = ns("Plot")) %>%
config(displaylogo = FALSE)
if (input$style == "Histogram") {
plot_plotly <- config(plot_plotly, modeBarButtonsToRemove = list("select2d","lasso2d"))
}
} else {
plot_plotly <- plot_ly(x = 1, y = 1, type = 'scatter', mode = 'text',
text = 'This plot type is not available as interactive plot. <br> Please see the "Print" tap instead.',
textposition = 'middle center', textfont = list(color = '#000000', size = 16)) %>%
layout(xaxis = list(title = "", zeroline = FALSE, showline = FALSE, showticklabels = FALSE, showgrid = FALSE),
yaxis = list(title = "", zeroline = FALSE, showline = FALSE, showticklabels = FALSE, showgrid = FALSE))
}
if (!input$style %in% c("Boxplot", "Violin")) {
if (str_detect(x()[[1]], "Model")) {plot_plotly <- plot_plotly %>% layout(xaxis = list(autorange = "reversed"))}
if (!is.null(y()) && str_detect(y()[[1]], "Model")) {plot_plotly <- plot_plotly %>% layout(yaxis = list(autorange = "reversed"))}
if (!is.null(z()) && str_detect(z()[[1]], "Model")) {plot_plotly <- plot_plotly %>% layout(zaxis = list(autorange = "reversed"))}
} else {
if (str_detect(x()[[1]], "Model")) {plot_plotly <- plot_plotly %>% layout(yaxis = list(autorange = "reversed"))}
}
for (i in 1:length(plot_plotly$x$data)){
if (!is.null(plot_plotly$x$data[[i]]$name)){
plot_plotly$x$data[[i]]$name <- gsub("\\(","",str_split(plot_plotly$x$data[[i]]$name,",")[[1]][1])
}
}
plot_plotly
})
output$plot_data <- DT::renderDataTable({
plot_coords <- event_data("plotly_brushed", source = ns("Plot"))
if (is.null(plot_coords)) return(NULL)
data_view <- data_reference() %>%
filter(between(!!as.symbol(x()[[1]]), plot_coords[["x"]][1], plot_coords[["x"]][2])) %>%
filter(between(!!as.symbol(y()[[1]]), plot_coords[["y"]][1], plot_coords[["y"]][2]))
DT::datatable(data_view %>% select(-contains("20"), -Reference, -doi, -Note, -Latitude, -Longitude, -year, -contains("_"), -tooltip),
rownames = FALSE, options = list(scrollX = TRUE))
})
plot_export <- reactive({
req(plot())
plot_export <- plot()
if ("ggplot" %in% class(plot_export)) {
if (!is.null(y())) {plot_export <- plot_export + labs(y = y()[[3]])}
if (input$style == "2D Scatter") {plot_export <- plot_export + labs(color = z()[[3]])}
if (!input$style %in% c("Boxplot", "Violin")) {
if (str_detect(x()[[1]], "Model")) {plot_export <- plot_export + scale_x_reverse()}
if (!is.null(y()) && str_detect(y()[[1]], "Model")) {plot_export <- plot_export + scale_y_reverse()}
if (plot_export[["labels"]][["x"]] == x()[[2]]) {plot_export <- plot_export + labs(x = x()[[3]])}
} else {
if (str_detect(x()[[1]], "Model")) {plot_export <- plot_export + scale_y_reverse()}
if (plot_export[["labels"]][["y"]] == x()[[2]]) {plot_export <- plot_export + labs(y = x()[[3]])}
}
} else {
plot_export <- ggplot(mapping = aes(x = c(1, 0), y = c(0, 1), colour = c("A", "B"))) +
geom_point(alpha = 0) +
annotate(geom = "text", x = 0.5, y = 0.5, label = str_wrap("3D Scatterplots cannot be downloaded. Please use the snapshot tool in the interactive plot instead.", width = 40), size = 5) +
theme_void() +
theme(legend.position = "none",
legend.text=element_text(color = "white")
)
}
plot_export
})
output$plot_print <- renderPlot({ plot_export() })
return(plot_export)
}
)
}