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Change size to linewidth (except for geom_point and element_text) #205

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Change size to linewidth (except for geom_point and element_text) #205

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ Imports:
colourpicker,
DT (>= 0.2),
dygraphs (>= 1.1.1.2),
ggplot2 (>= 2.1.1),
ggplot2 (>= 3.4.0),
gridExtra,
gtools,
markdown (>= 0.7.4),
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8 changes: 4 additions & 4 deletions inst/ShinyStan/helper_functions/gg_theme_elements.R
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Expand Up @@ -20,8 +20,8 @@ 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)
axis.line.x = element_line(linewidth = 3, color = axis_line_color),
axis.line.y = element_line(linewidth = 0.5, color = axis_line_color)
)
no_yaxs <- theme(
axis.line.y = element_blank(),
Expand All @@ -38,11 +38,11 @@ strip_txt <- theme(

# horizontal and vertical lines -------------------------------------------
h_lines <- theme(
panel.grid.major = element_line(size = 0.10, linetype = 3, color = "turquoise4"),
panel.grid.major = element_line(linewidth = 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 = element_line(linewidth = 0.25, linetype = 3, color = "turquoise4"),
panel.grid.major.y = element_blank()
)

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12 changes: 6 additions & 6 deletions inst/ShinyStan/helper_functions/hmc_diagnostics_helpers.R
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Expand Up @@ -110,14 +110,14 @@ thm_no_yaxs <- thm + no_yaxs
base <- ggplot(mdf, aes(x = value)) +
geom_histogram(aes_string(y="..density.."),
binwidth = diff(range(mdf$value))/30, fill = base_fill,
color = vline_base_clr, size = 0.2) +
color = vline_base_clr, linewidth = 0.2) +
labs(x = if (missing(lab)) NULL else lab, y = "") +
thm

if (chain == 0) {
graph <- base +
geom_vline(xintercept = mean(mdf$value), color = vline_base_clr, size = .8) +
geom_vline(xintercept = median(mdf$value), color = vline_base_clr, lty = 2, size = 1)
geom_vline(xintercept = mean(mdf$value), color = vline_base_clr, linewidth = .8) +
geom_vline(xintercept = median(mdf$value), color = vline_base_clr, lty = 2, linewidth = 1)
return(graph)
}
chain_data <- subset(mdf, variable == paste0("chain:",chain))
Expand All @@ -127,9 +127,9 @@ thm_no_yaxs <- thm + no_yaxs
aes_string(y="..density.."),
binwidth = diff(range(chain_data$value))/30,
fill = chain_fill, alpha = 0.5) +
geom_vline(xintercept = mean(chain_data$value), color = chain_clr, size = .8) +
geom_vline(xintercept = mean(chain_data$value), color = chain_clr, linewidth = .8) +
geom_vline(xintercept = median(chain_data$value),
color = chain_clr, lty = 2, size = 1)
color = chain_clr, lty = 2, linewidth = 1)
}

.treedepth_ndivergent_hist <- function(df_td, df_nd, chain = 0, divergent = c("All", 0, 1)) {
Expand All @@ -148,7 +148,7 @@ thm_no_yaxs <- thm + no_yaxs

graph <- ggplot(plot_data, aes(x = factor(value)), na.rm = TRUE) +
geom_bar(aes(y=..count../sum(..count..)), width=1, fill = base_fill,
color = vline_base_clr, size = 0.2) +
color = vline_base_clr, linewidth = 0.2) +
plot_labs +
plot_theme
if (chain == 0)
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26 changes: 13 additions & 13 deletions inst/ShinyStan/helper_functions/shinystan_helpers.R
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Expand Up @@ -39,7 +39,7 @@
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) + scale_x_continuous(limits = c(x1, x2))
graph <- graph + geom_line(linewidth = 0.35) + scale_x_continuous(limits = c(x1, x2))

if (layout == "Grid") {
graph <- graph + facet_wrap(~ parameters, scales = "free_y")
Expand Down Expand Up @@ -76,10 +76,10 @@
graph <- ggplot(dat, aes(x = value))

if (binwd == 0) {
graph <- graph + geom_histogram(fill = fill_color, color = line_color, size = 0.2)
graph <- graph + geom_histogram(fill = fill_color, color = line_color, linewidth = 0.2)
} else {
graph <- graph + geom_histogram(fill = fill_color, color = line_color,
binwidth = binwd, size = 0.2)
binwidth = binwd, linewidth = 0.2)
}
graph <- graph +
labs(x = x_lab, y = "") +
Expand Down Expand Up @@ -266,7 +266,7 @@ priors <- data.frame(family = c("Normal", "t", "Cauchy", "Beta", "Exponential",
graph <- ggplot(ac_dat, aes(x= lag, y = ac))
graph <- graph +
geom_bar(position = "identity", stat = "identity",
fill = base_fill, size = 0.4) +
fill = base_fill, linewidth = 0.4) +
y_scale +
ac_labs +
ac_theme
Expand All @@ -278,7 +278,7 @@ priors <- data.frame(family = c("Normal", "t", "Cauchy", "Beta", "Exponential",
graph <- ggplot(ac_dat, aes(x = lag, y = ac, color = factor(chains),
fill = factor(chains)))
graph <- graph +
geom_bar(position = "identity", stat = "identity", size = 0.4) +
geom_bar(position = "identity", stat = "identity", linewidth = 0.4) +
scale_fill_manual(values = rep(base_fill, nChains)) +
scale_color_manual(values = rep(vline_base_clr, nChains)) +
y_scale +
Expand Down Expand Up @@ -372,10 +372,10 @@ priors <- data.frame(family = c("Normal", "t", "Cauchy", "Beta", "Exponential",
axis.ticks.y = element_blank(),
axis.text= element_text(size=12),
axis.text.y= element_text(face = "bold"),
axis.line= element_line(size = 4, color = axis_line_color),
axis.line.y= element_line(size = 0.5, color = axis_line_color),
axis.line= element_line(linewidth = 4, color = axis_line_color),
axis.line.y= element_line(linewidth = 0.5, color = axis_line_color),
legend.position = "none",
panel.grid.major = element_line(size = 0.4),
panel.grid.major = element_line(linewidth = 0.4),
panel.grid.minor.y = element_blank())

p.all <- p.base + xlim(xlim.use) + p.name + theme_bw() + p.theme + transparent
Expand Down Expand Up @@ -424,18 +424,18 @@ priors <- data.frame(family = c("Normal", "t", "Cauchy", "Beta", "Exponential",
#point estimator
if (color_by_rhat) {
p.point <- geom_segment(aes(x = m, xend = m, y = y, yend = y + 0.25,
color = rhat_id), size = 1.5)
color = rhat_id), linewidth = 1.5)
p.all + p.poly + p.den + p.col + p.point + rhat_colors + rhat_lgnd
} else {
p.point <- geom_segment(aes(x = m, xend = m, y = y, yend = y + 0.25),
colour = est_color,
size = 1.5)
linewidth = 1.5)
p.all + p.poly + p.den + p.col + p.point
}

} else {
p.ci.2 <- geom_segment(aes(x = l, xend = h, y = y, yend = y),
colour = fill_color, size = 2)
colour = fill_color, linewidth = 2)
if (color_by_rhat) {
p.point <- geom_point(aes(x = m, y = y, fill = rhat_id), color = "black",
shape = 21, size = 4)
Expand All @@ -460,7 +460,7 @@ priors <- data.frame(family = c("Normal", "t", "Cauchy", "Beta", "Exponential",
my_labs <- labs(y = "", x = xlab)
base_fill
graph <- qplot(x = x, data = dat, color = I(vline_base_clr),
fill = I(base_fill), size = I(0.2))
fill = I(base_fill), linewidth = I(0.2))
graph <- graph +
my_labs +
theme_classic() %+replace% (axis_color + axis_labs + fat_axis + no_yaxs + transparent)
Expand Down Expand Up @@ -652,7 +652,7 @@ priors <- data.frame(family = c("Normal", "t", "Cauchy", "Beta", "Exponential",
}
if (ellipse_lev != "None")
graph <- graph + stat_ellipse(level = as.numeric(ellipse_lev), color = ellipse_color,
linetype = ellipse_lty, size = ellipse_lwd, alpha = ellipse_alpha)
linetype = ellipse_lty, linewidth = ellipse_lwd, alpha = ellipse_alpha)
if (!all(dat$divergent == 0))
graph <- graph + geom_point(data = subset(dat, divergent == 1), aes(x,y),
size = pt_size + 0.5, shape = 21,
Expand Down