R/PoDDyHePoPlot.R
In zzhhatthl/PoDDyHePo-projection: Projection Method for PoDDy-HePo Project
Defines functions
PoDDyHePoPlot
Documented in
PoDDyHePoPlot
#' Description of PoDDyHePoPlot()
#'
#' @title Plot Function Developed for PoDDy-Hepo Project
#'
#' @description It plots the prevalences against survey year.
#'
#' @details Enables plotting even there is a variable whose proportion of each category has been calculated.
#'
#' @param data A data frame from `PoDDyHePoPool()`.
#' @param year The maximum year in the observed data.
#' @param grplabels The labels of grouping variable. By default, grplabels = NULL. In our case, grplabels = c("Men", "Women").
#' @param title Title for the plot. It changes due to different response variable.
#' @param y_min minimum value of y-axis(in percentage). For example, if 10 percent is the minimum value of y-axis, then type let y_min = 10.
#' @param y_max maximum value of y-axis(in percentage). Let y_max = 75, if 75 percent is the maximum value of y-axis.
#' @param sepvarlbl Labels of the variable whose proportion of each category has been calculated. The default is \code{NULL}. If it is \code{NULL}, the name of variable will then be like obe_0, obe_1, obe_2 take our case for example. If it is labelled, as the levels are sorted, please make sure that the labels are in right order.
#'
#'
#' @return Returns a figure
#' @export
#'
#' @import ggplot2
PoDDyHePoPlot <- function(data, year, grplabels = NULL, title, y_min, y_max, sepvarlbl = NULL){
if(ncol(data) == 4){
if(!is.null(grplabels)){
cat("Not using a grouping variable, there should not be grplabels. \n However, programme continue...")
}
ggplot(data = data[data$Year <= year, ], aes(x = .data$Year, y = 100 * .data$EST)) +
geom_line(size = 0.65, position = position_dodge(width = 1.5), color = "blue") +
geom_line(data = data[data$Year >= year, ], linetype = "dashed", size = 0.65, position = position_dodge(width = 1.5), color = "blue") +
geom_point(size = 3, position = position_dodge(width = 1.5), color = "blue") +
geom_point(data = data[data$Year > year, ], size = 3, position = position_dodge(width = 1.5), color = "blue") +
geom_errorbar(aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 1.5,
position = position_dodge(width = 1.5),
color = "blue") +
geom_errorbar(data = data[data$Year > year, ],
aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 1.5,
position = position_dodge(width = 1.5),
color = "blue") +
scale_y_continuous(name = "%",
limits = c(y_min, y_max),
breaks = c(seq(0, floor(y_max/10)*10, 10), y_max)) +
scale_x_continuous(breaks = unique(data$Year)) +
theme_bw() +
ggtitle(title) +
theme(plot.title = element_text(hjust = 0.5 ,margin = margin(5, 0, 15, 0), size = 28),
axis.title.x = element_text(margin = margin(5, 0, 5, 0), size = 22),
axis.text.x = element_text(size = 16, angle = 45, vjust = 0.5),
axis.title.y = element_text(margin = margin(0, 5, 0, 10), size = 22),
axis.text.y = element_text(size = 18),
legend.title = element_text(size = 16),
legend.text = element_text(size = 24),
legend.margin = margin(0, 0, 0, 0),
panel.grid.minor = element_blank()) +
theme(aspect.ratio = 2/3)
} else if(ncol(data) == 5 & "Group" %in% names(data)){
if(!is.null(grplabels)){
cat("Not using a grouping variable, there should not be grplabels. \n However, programme continue...")
}
# Levels for seperated variable
levels <- sort(unique(data$Group))
# Label seperated variable
if(is.null(sepvarlbl)){
sepvarlbl <- levels
}
data$Group <- factor(data$Group,
labels = sepvarlbl,
levels = levels)
# Plot
ggplot(data = data[data$Year <= year, ], aes(x = .data$Year, y = 100 * .data$EST, color = .data$Group, group = .data$Group)) +
geom_point(aes(shape = .data$Group), size = 2.5, position = position_dodge(width = 2.5)) +
geom_point(aes(shape = .data$Group), data = data[data$Year > year, ], size = 2.5, position = position_dodge(width = 2.5)) +
geom_line(size = 0.65, position = position_dodge(width = 2.5)) +
geom_line(data = data[data$Year >= year, ], linetype = "dashed", size = 0.65, position = position_dodge(width = 2.5)) +
geom_errorbar(aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 3,
position = position_dodge(width = 2.5)) +
geom_errorbar(data = data[data$Year > year, ],
aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 3,
position = position_dodge(width = 2.5)) +
scale_y_continuous(name = "%",
limits = c(y_min, y_max),
breaks = c(seq(0, floor(y_max/10)*10, 10), y_max)) +
scale_x_continuous(breaks = unique(data$Year)) +
scale_shape_manual(name = " ",
labels = sepvarlbl,
values = c(21, 24, 22, 23, 25)) +
ggtitle(title) +
scale_color_manual(name = " ",
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62"),
guide = "none") +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5 ,margin = margin(5, 0, 15, 0), size = 28),
axis.title.x = element_text(margin = margin(5, 0, 5, 0), size = 20),
axis.text.x = element_text(size = 14, angle = 45, vjust = 0.5),
axis.title.y = element_text(margin = margin(0, 5, 0, 10), size = 20),
axis.text.y = element_text(size = 18),
legend.title = element_text(size = 16),
legend.text = element_text(size = 20),
legend.margin = margin(0, 0, 0, 0),
strip.text.x = element_text(size = 18),
strip.background = element_rect(fill = "gray95", color = "black"),
panel.border = element_rect(color = "black"),
panel.spacing = unit(0.35, "lines"),
panel.grid.minor = element_blank()) +
theme(aspect.ratio = 2/3)
} else if(ncol(data) == 5 & !"Group" %in% names(data)){
if(is.null(grplabels)){
cat("Grouping variable applied, it would be better if grplabels specified. \n")
}
grpVar <- names(data)[!names(data) %in% c("Year", "EST", "CI_LOWER", "CI_UPPER")]
# Plot (not seperated variable)
ggplot(data = data[data$Year <= year, ], aes(x = .data$Year, y = 100 * .data$EST, color = .data[[grpVar]])) +
geom_line(size = 0.65, position = position_dodge(width = 1.5)) +
geom_line(data = data[data$Year >= year, ], linetype = "dashed", size = 0.65, position = position_dodge(width = 1.5)) +
geom_point(aes(fill = .data[[grpVar]], shape = .data$.data[[names(data)[!names(data) %in% c("Year", "EST", "CI_LOWER", "CI_UPPER")]]]), size = 3, position = position_dodge(width = 1.5)) +
geom_point(aes(shape = .data[[grpVar]]), data = data[data$Year > year, ], size = 3, position = position_dodge(width = 1.5)) +
geom_errorbar(aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 1.5,
position = position_dodge(width = 1.5)) +
geom_errorbar(data = data[data$Year > year, ],
aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 1.5,
position = position_dodge(width = 1.5)) +
scale_y_continuous(name = "%",
limits = c(y_min, y_max),
breaks = c(seq(0, floor(y_max/10)*10, 10), y_max)) +
scale_x_continuous(breaks = unique(data$Year)) +
scale_color_manual(name = " ",
labels = grplabels,
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62")) +
scale_shape_manual(name = " ",
labels = grplabels,
values = c(21, 24, 22, 23, 25)) +
scale_fill_manual(guide = "none",
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62")) +
theme_bw() +
ggtitle("title") +
theme(plot.title = element_text(hjust = 0.5 ,margin = margin(5, 0, 15, 0), size = 28),
axis.title.x = element_text(margin = margin(5, 0, 5, 0), size = 22),
axis.text.x = element_text(size = 16, angle = 45, vjust = 0.5),
axis.title.y = element_text(margin = margin(0, 5, 0, 10), size = 22),
axis.text.y = element_text(size = 18),
legend.title = element_text(size = 16),
legend.text = element_text(size = 24),
legend.margin = margin(0, 0, 0, 0),
panel.grid.minor = element_blank()) +
theme(aspect.ratio = 2/3)
} else{
colnames(data) <- c("Year", "grpVar", "EST", "CI_LOWER", "CI_UPPER", "Group")
if(is.null(grplabels)){
grplabels <- sort(unique(data$grpVar))
cat("Grouping variable applied, it would be better if grplabels specified. \n")
}
# Levels for seperated variable
levels <- sort(unique(data$Group))
# Label seperated variable
if(is.null(sepvarlbl)){
sepvarlbl <- levels
}
data$Group <- factor(data$Group,
labels = sepvarlbl,
levels = levels)
# Label grouping variable
data$grpVar <- factor(data$grpVar,
levels = sort(unique(data$grpVar)),
labels = grplabels)
# Plot
ggplot(data = data[data$Year <= year, ], aes(x = .data$Year, y = 100 * .data$EST, color = .data$grpVar, group = .data$Group)) +
geom_point(aes(fill = .data$grpVar, shape = .data$Group), size = 2.5, position = position_dodge(width = 2.5)) +
geom_point(aes(shape = .data$Group), data = data[data$Year > year, ], size = 2.5, position = position_dodge(width = 2.5)) +
geom_line(size = 0.65, position = position_dodge(width = 2.5)) +
geom_line(data = data[data$Year >= year, ], linetype = "dashed", size = 0.65, position = position_dodge(width = 2.5)) +
geom_errorbar(aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 3,
position = position_dodge(width = 2.5)) +
geom_errorbar(data = data[data$Year > year, ],
aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 3,
position = position_dodge(width = 2.5)) +
scale_y_continuous(name = "%",
limits = c(y_min, y_max),
breaks = c(seq(0, floor(y_max/10)*10, 10), y_max)) +
scale_x_continuous(breaks = unique(data$Year)) +
scale_shape_manual(name = " ",
labels = sepvarlbl,
values = c(21, 24, 22, 23, 25)) +
scale_fill_manual(guide = "none",
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62")) +
ggtitle("title") +
facet_wrap( ~ grpVar) +
scale_color_manual(name = " ",
labels = c("Men", "Women"),
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62"),
guide = "none") +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5 ,margin = margin(5, 0, 15, 0), size = 28),
axis.title.x = element_text(margin = margin(5, 0, 5, 0), size = 20),
axis.text.x = element_text(size = 14, angle = 45, vjust = 0.5),
axis.title.y = element_text(margin = margin(0, 5, 0, 10), size = 20),
axis.text.y = element_text(size = 18),
legend.title = element_text(size = 16),
legend.text = element_text(size = 20),
legend.margin=margin(0, 0, 0, 0),
strip.text.x = element_text(size = 18),
strip.background = element_rect(fill = "gray95", color = "black"),
panel.border = element_rect(color = "black"),
panel.spacing = unit(0.35, "lines"),
panel.grid.minor = element_blank())
}
}
zzhhatthl/PoDDyHePo-projection documentation built on June 16, 2022, 12:47 p.m.
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Defines functions PoDDyHePoPlot
Documented in PoDDyHePoPlot
#' Description of PoDDyHePoPlot()
#'
#' @title Plot Function Developed for PoDDy-Hepo Project
#'
#' @description It plots the prevalences against survey year.
#'
#' @details Enables plotting even there is a variable whose proportion of each category has been calculated.
#'
#' @param data A data frame from `PoDDyHePoPool()`.
#' @param year The maximum year in the observed data.
#' @param grplabels The labels of grouping variable. By default, grplabels = NULL. In our case, grplabels = c("Men", "Women").
#' @param title Title for the plot. It changes due to different response variable.
#' @param y_min minimum value of y-axis(in percentage). For example, if 10 percent is the minimum value of y-axis, then type let y_min = 10.
#' @param y_max maximum value of y-axis(in percentage). Let y_max = 75, if 75 percent is the maximum value of y-axis.
#' @param sepvarlbl Labels of the variable whose proportion of each category has been calculated. The default is \code{NULL}. If it is \code{NULL}, the name of variable will then be like obe_0, obe_1, obe_2 take our case for example. If it is labelled, as the levels are sorted, please make sure that the labels are in right order.
#'
#'
#' @return Returns a figure
#' @export
#'
#' @import ggplot2
PoDDyHePoPlot <- function(data, year, grplabels = NULL, title, y_min, y_max, sepvarlbl = NULL){
if(ncol(data) == 4){
if(!is.null(grplabels)){
cat("Not using a grouping variable, there should not be grplabels. \n However, programme continue...")
}
ggplot(data = data[data$Year <= year, ], aes(x = .data$Year, y = 100 * .data$EST)) +
geom_line(size = 0.65, position = position_dodge(width = 1.5), color = "blue") +
geom_line(data = data[data$Year >= year, ], linetype = "dashed", size = 0.65, position = position_dodge(width = 1.5), color = "blue") +
geom_point(size = 3, position = position_dodge(width = 1.5), color = "blue") +
geom_point(data = data[data$Year > year, ], size = 3, position = position_dodge(width = 1.5), color = "blue") +
geom_errorbar(aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 1.5,
position = position_dodge(width = 1.5),
color = "blue") +
geom_errorbar(data = data[data$Year > year, ],
aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 1.5,
position = position_dodge(width = 1.5),
color = "blue") +
scale_y_continuous(name = "%",
limits = c(y_min, y_max),
breaks = c(seq(0, floor(y_max/10)*10, 10), y_max)) +
scale_x_continuous(breaks = unique(data$Year)) +
theme_bw() +
ggtitle(title) +
theme(plot.title = element_text(hjust = 0.5 ,margin = margin(5, 0, 15, 0), size = 28),
axis.title.x = element_text(margin = margin(5, 0, 5, 0), size = 22),
axis.text.x = element_text(size = 16, angle = 45, vjust = 0.5),
axis.title.y = element_text(margin = margin(0, 5, 0, 10), size = 22),
axis.text.y = element_text(size = 18),
legend.title = element_text(size = 16),
legend.text = element_text(size = 24),
legend.margin = margin(0, 0, 0, 0),
panel.grid.minor = element_blank()) +
theme(aspect.ratio = 2/3)
} else if(ncol(data) == 5 & "Group" %in% names(data)){
if(!is.null(grplabels)){
cat("Not using a grouping variable, there should not be grplabels. \n However, programme continue...")
}
# Levels for seperated variable
levels <- sort(unique(data$Group))
# Label seperated variable
if(is.null(sepvarlbl)){
sepvarlbl <- levels
}
data$Group <- factor(data$Group,
labels = sepvarlbl,
levels = levels)
# Plot
ggplot(data = data[data$Year <= year, ], aes(x = .data$Year, y = 100 * .data$EST, color = .data$Group, group = .data$Group)) +
geom_point(aes(shape = .data$Group), size = 2.5, position = position_dodge(width = 2.5)) +
geom_point(aes(shape = .data$Group), data = data[data$Year > year, ], size = 2.5, position = position_dodge(width = 2.5)) +
geom_line(size = 0.65, position = position_dodge(width = 2.5)) +
geom_line(data = data[data$Year >= year, ], linetype = "dashed", size = 0.65, position = position_dodge(width = 2.5)) +
geom_errorbar(aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 3,
position = position_dodge(width = 2.5)) +
geom_errorbar(data = data[data$Year > year, ],
aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 3,
position = position_dodge(width = 2.5)) +
scale_y_continuous(name = "%",
limits = c(y_min, y_max),
breaks = c(seq(0, floor(y_max/10)*10, 10), y_max)) +
scale_x_continuous(breaks = unique(data$Year)) +
scale_shape_manual(name = " ",
labels = sepvarlbl,
values = c(21, 24, 22, 23, 25)) +
ggtitle(title) +
scale_color_manual(name = " ",
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62"),
guide = "none") +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5 ,margin = margin(5, 0, 15, 0), size = 28),
axis.title.x = element_text(margin = margin(5, 0, 5, 0), size = 20),
axis.text.x = element_text(size = 14, angle = 45, vjust = 0.5),
axis.title.y = element_text(margin = margin(0, 5, 0, 10), size = 20),
axis.text.y = element_text(size = 18),
legend.title = element_text(size = 16),
legend.text = element_text(size = 20),
legend.margin = margin(0, 0, 0, 0),
strip.text.x = element_text(size = 18),
strip.background = element_rect(fill = "gray95", color = "black"),
panel.border = element_rect(color = "black"),
panel.spacing = unit(0.35, "lines"),
panel.grid.minor = element_blank()) +
theme(aspect.ratio = 2/3)
} else if(ncol(data) == 5 & !"Group" %in% names(data)){
if(is.null(grplabels)){
cat("Grouping variable applied, it would be better if grplabels specified. \n")
}
grpVar <- names(data)[!names(data) %in% c("Year", "EST", "CI_LOWER", "CI_UPPER")]
# Plot (not seperated variable)
ggplot(data = data[data$Year <= year, ], aes(x = .data$Year, y = 100 * .data$EST, color = .data[[grpVar]])) +
geom_line(size = 0.65, position = position_dodge(width = 1.5)) +
geom_line(data = data[data$Year >= year, ], linetype = "dashed", size = 0.65, position = position_dodge(width = 1.5)) +
geom_point(aes(fill = .data[[grpVar]], shape = .data$.data[[names(data)[!names(data) %in% c("Year", "EST", "CI_LOWER", "CI_UPPER")]]]), size = 3, position = position_dodge(width = 1.5)) +
geom_point(aes(shape = .data[[grpVar]]), data = data[data$Year > year, ], size = 3, position = position_dodge(width = 1.5)) +
geom_errorbar(aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 1.5,
position = position_dodge(width = 1.5)) +
geom_errorbar(data = data[data$Year > year, ],
aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 1.5,
position = position_dodge(width = 1.5)) +
scale_y_continuous(name = "%",
limits = c(y_min, y_max),
breaks = c(seq(0, floor(y_max/10)*10, 10), y_max)) +
scale_x_continuous(breaks = unique(data$Year)) +
scale_color_manual(name = " ",
labels = grplabels,
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62")) +
scale_shape_manual(name = " ",
labels = grplabels,
values = c(21, 24, 22, 23, 25)) +
scale_fill_manual(guide = "none",
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62")) +
theme_bw() +
ggtitle("title") +
theme(plot.title = element_text(hjust = 0.5 ,margin = margin(5, 0, 15, 0), size = 28),
axis.title.x = element_text(margin = margin(5, 0, 5, 0), size = 22),
axis.text.x = element_text(size = 16, angle = 45, vjust = 0.5),
axis.title.y = element_text(margin = margin(0, 5, 0, 10), size = 22),
axis.text.y = element_text(size = 18),
legend.title = element_text(size = 16),
legend.text = element_text(size = 24),
legend.margin = margin(0, 0, 0, 0),
panel.grid.minor = element_blank()) +
theme(aspect.ratio = 2/3)
} else{
colnames(data) <- c("Year", "grpVar", "EST", "CI_LOWER", "CI_UPPER", "Group")
if(is.null(grplabels)){
grplabels <- sort(unique(data$grpVar))
cat("Grouping variable applied, it would be better if grplabels specified. \n")
}
# Levels for seperated variable
levels <- sort(unique(data$Group))
# Label seperated variable
if(is.null(sepvarlbl)){
sepvarlbl <- levels
}
data$Group <- factor(data$Group,
labels = sepvarlbl,
levels = levels)
# Label grouping variable
data$grpVar <- factor(data$grpVar,
levels = sort(unique(data$grpVar)),
labels = grplabels)
# Plot
ggplot(data = data[data$Year <= year, ], aes(x = .data$Year, y = 100 * .data$EST, color = .data$grpVar, group = .data$Group)) +
geom_point(aes(fill = .data$grpVar, shape = .data$Group), size = 2.5, position = position_dodge(width = 2.5)) +
geom_point(aes(shape = .data$Group), data = data[data$Year > year, ], size = 2.5, position = position_dodge(width = 2.5)) +
geom_line(size = 0.65, position = position_dodge(width = 2.5)) +
geom_line(data = data[data$Year >= year, ], linetype = "dashed", size = 0.65, position = position_dodge(width = 2.5)) +
geom_errorbar(aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 3,
position = position_dodge(width = 2.5)) +
geom_errorbar(data = data[data$Year > year, ],
aes(ymin = 100 * .data$CI_LOWER,
ymax = 100 * .data$CI_UPPER),
width = 3,
position = position_dodge(width = 2.5)) +
scale_y_continuous(name = "%",
limits = c(y_min, y_max),
breaks = c(seq(0, floor(y_max/10)*10, 10), y_max)) +
scale_x_continuous(breaks = unique(data$Year)) +
scale_shape_manual(name = " ",
labels = sepvarlbl,
values = c(21, 24, 22, 23, 25)) +
scale_fill_manual(guide = "none",
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62")) +
ggtitle("title") +
facet_wrap( ~ grpVar) +
scale_color_manual(name = " ",
labels = c("Men", "Women"),
values = c("blue", "red", "black", "#61D04F", "#28E2E5", "#CD0BBC", "#F5C710", "gray62"),
guide = "none") +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5 ,margin = margin(5, 0, 15, 0), size = 28),
axis.title.x = element_text(margin = margin(5, 0, 5, 0), size = 20),
axis.text.x = element_text(size = 14, angle = 45, vjust = 0.5),
axis.title.y = element_text(margin = margin(0, 5, 0, 10), size = 20),
axis.text.y = element_text(size = 18),
legend.title = element_text(size = 16),
legend.text = element_text(size = 20),
legend.margin=margin(0, 0, 0, 0),
strip.text.x = element_text(size = 18),
strip.background = element_rect(fill = "gray95", color = "black"),
panel.border = element_rect(color = "black"),
panel.spacing = unit(0.35, "lines"),
panel.grid.minor = element_blank())
}
}
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