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Feature/issue 17 multitrace yscale #48

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Mar 14, 2015
Merged

Feature/issue 17 multitrace yscale #48

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fd69e4f
fix multitrace yscale not adjusting
jgabry Mar 14, 2015
3e7a3e7
update .param_trace_multi
jgabry Mar 14, 2015
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36 changes: 17 additions & 19 deletions inst/shinyStan/helper_functions/shinyStan_helpers.R
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ axis_labs <- theme(axis.title = element_text(face = "bold", size = 13))
title_txt <- theme(plot.title = element_text(face = "bold", size = 14))
fat_axis <- theme(axis.line.x = element_line(size = 3, color = axis_line_color),
axis.line.y = element_line(size = 0.5, color = axis_line_color))
h_lines <- theme(panel.grid.major = element_line(size = 0.25, linetype = 3, color = "turquoise4"),
h_lines <- theme(panel.grid.major = element_line(size = 0.10, linetype = 3, color = "turquoise4"),
panel.grid.major.x = element_blank())
v_lines <- theme(panel.grid.major = element_line(size = 0.25, linetype = 3, color = "turquoise4"),
panel.grid.major.y = element_blank())
Expand Down Expand Up @@ -281,9 +281,9 @@ strip_txt <- theme(strip.text = element_text(size = 12, face = "bold", color = "
if(palette == "Rainbow") clrs <- scale_colour_manual(values = rainbow(nclrs))

theme_elements <- axis_color + fat_axis + no_lgnd + axis_labs + transparent
if (style == "line") theme_elements <- theme_elements + h_lines
# if (style == "line") theme_elements <- theme_elements + h_lines
graph <- ggplot(dat, aes(x = iterations, y = value, color = chains))
graph <- graph + xy_labs + clrs + theme_classic() %+replace% theme_elements # (fat_axis + h_lines + no_lgnd)
graph <- graph + xy_labs + clrs + theme_classic() %+replace% theme_elements
if (rect != "None") graph <- graph + shading_rect
if (rect == "None" & inc_warmup) graph <- graph + geom_vline(xintercept = warmup_val, color = "gray35", size = 1.5)

Expand All @@ -309,24 +309,24 @@ strip_txt <- theme(strip.text = element_text(size = 12, face = "bold", color = "
# param_trace_multi ------------------------------------------------------
# trace plots for multiple parameters
.param_trace_multi <- function(params = NULL, all_param_names, dat, warmup_val = 0,
inc_warmup = TRUE, chain = 0, palette = "Default",
chain = 0, palette = "Default",
rect = "Samples", rect_color = "skyblue", rect_alpha = 0.1,
layout = "Long", x1, x2) {


params <- .update_params_with_groups(params, all_param_names)
if(length(params) == 0) {
params <- dimnames(dat)$parameters[1:min(4, dim(dat)[3])]
}
params <- unique(params)
dat <- reshape2::melt(dat)
dat <- subset(dat, parameters %in% params)
dat <- reshape2::melt(dat[,,params, drop=FALSE])

if (!("chains" %in% colnames(dat))) { # fixes for if there's only 1 chain:
dat$chains <- "chain:1"
dat$iterations <- 1:nrow(dat)
}

dat$iterations <- x1:x2

if (!inc_warmup) dat <- subset(dat, iterations >= warmup_val)
if (chain != 0) dat <- subset(dat, chains == paste0("chain:",chain))

rect_xmin <- ifelse(rect == "Samples", Inf, -Inf)
Expand All @@ -336,26 +336,24 @@ strip_txt <- theme(strip.text = element_text(size = 12, face = "bold", color = "
xy_labs <- labs(y = "Value", x = "Iteration")
nclrs <- length(unique(dat$chains))

ldgn_title <- ""
if(palette == "Default") clrs <- scale_color_discrete(name = ldgn_title)
if(palette == "Gray") clrs <- scale_color_grey(name = ldgn_title)
if(palette == "Brewer (spectral)") clrs <- scale_color_brewer(name = ldgn_title, palette = "Spectral")
if(palette == "Rainbow") clrs <- scale_colour_manual(name = ldgn_title, values = rainbow(nclrs))
lgnd_title <- ""
if(palette == "Default") clrs <- scale_color_discrete(name = lgnd_title)
if(palette == "Gray") clrs <- scale_color_grey(name = lgnd_title)
if(palette == "Brewer (spectral)") clrs <- scale_color_brewer(name = lgnd_title, palette = "Spectral")
if(palette == "Rainbow") clrs <- scale_colour_manual(name = lgnd_title, values = rainbow(nclrs))


lgnd_txt <- theme(legend.text = element_text(size = 13, face = "bold"))

graph <- ggplot(dat, aes(x = iterations, y = value, color = chains))
graph <- graph + xy_labs + clrs + theme_classic() %+replace% (axis_color + axis_labs + fat_axis + h_lines + lgnd_top + lgnd_txt + strip_txt + transparent)
if (rect != "None") graph <- graph + shading_rect
graph <- graph + geom_line(size = 0.35)
if (!is.na(x1)) {
graph <- graph + scale_x_continuous(limits = c(x1, x2))
}
graph <- graph + geom_line(size = 0.35) + scale_x_continuous(limits = c(x1, x2))

if (layout == "Grid") {
graph <- graph + facet_wrap(~ parameters, scale = "free_y")
graph <- graph + facet_wrap(~ parameters, scales = "free_y")
} else {
graph <- graph + facet_grid(parameters ~., scale = "free_y")
graph <- graph + facet_grid(parameters ~., scales = "free_y")
}

graph
Expand Down
2 changes: 1 addition & 1 deletion inst/shinyStan/server_files/dynamic_ui/ui_warnings_customize.R
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
output$ui_warnings_customize <- renderUI({

absolutePanel(id = "controls_warnings", class = "panel panel-default hvr-glow", fixed = TRUE,
top = 100, right = 20, width = 270,
top = 150, right = 20, width = 270,
draggable = TRUE,
div(class = "shinystan_customize", "shinyStan customize"),
wellPanel(style = "background-color: #222222; padding-top: 10px ; padding-bottom: 0px;",
Expand Down
13 changes: 9 additions & 4 deletions inst/shinyStan/server_files/outputs/multi_trace_plot_reactive.R
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Original file line number Diff line number Diff line change
Expand Up @@ -20,21 +20,26 @@ calc_height_trace_plot <- reactive({
multi_trace_plot <- reactive({

validate(need(!is.null(input$multi_trace_rect), message = "Loading..."))

x1 <- input$multi_xzoom[1]
x2 <- input$multi_xzoom[2]

dat <- samps_all[x1:x2,,,drop=FALSE]


# zoom <- "On"
do.call(".param_trace_multi", args = list(
params = input$multi_trace_params,
all_param_names = param_names,
dat = samps_all,
dat = dat,
chain = input$multi_trace_chain,
warmup_val = warmup_val,
inc_warmup = TRUE, # input$multi_trace_warmup == "include",
palette = input$multi_trace_palette ,
rect = input$multi_trace_rect,
rect_color = "skyblue",
rect_alpha = input$multi_trace_rect_alpha,
layout = input$multi_trace_layout,
x1 = input$multi_xzoom[1],
x2 = input$multi_xzoom[2]
x1 = x1,
x2 = x2
))
})
2 changes: 1 addition & 1 deletion inst/shinyStan/ui.R
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Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,7 @@ navbarPage(title = strong(style = "color: #f9dd67; ", "shinyStan"),
wellPanel(
fluidRow(
column(6,selectizeInput("multi_trace_params", width = '100%', label = h5("Select or enter parameter names"), choices = .make_param_list_with_groups(object), multiple = TRUE)),
column(3, offset = 1, sliderInput("multi_xzoom", width = "75%",label = h5("Iterations range"), min = 0, max = object@nIter, step = 1, value = c(object@nWarmup + 1, object@nIter), ticks = FALSE)),
column(3, offset = 1, sliderInput("multi_xzoom", width = "75%",label = h5("Iterations range"), min = 1, max = object@nIter, step = 1, value = c(object@nWarmup + 1, object@nIter), ticks = FALSE)),
column(2, tags$div(h5("Customize"),includeHTML("html/multi_trace_options.html")))
)
),
Expand Down