mirror of
https://github.com/agdamsbo/stRoke.git
synced 2024-10-29 19:01:53 +01:00
87 lines
2.7 KiB
R
87 lines
2.7 KiB
R
utils::globalVariables(c("name","value","facet"))
|
|
#' Plot multidimensional cognitive test scores
|
|
#'
|
|
#' Plot index scores from five dimensional cognitive testing.
|
|
#' Includes option to facet.
|
|
#'
|
|
#' @param ds complete data frame
|
|
#' @param id colname of id column. Base for colouring
|
|
#' @param sub_plot main outcome scores variable to plot
|
|
#' @param scores variables to subset for plotting. Has to follow standard
|
|
#' naming (is to be changed)
|
|
#' @param dom_names domain names for axis naming
|
|
#' @param facet.by variable to base facet_grid on
|
|
#'
|
|
#' @return ggplot element
|
|
#'
|
|
#' @import ggplot2
|
|
#' @importFrom dplyr mutate
|
|
#' @importFrom dplyr select
|
|
#' @importFrom tidyr pivot_longer
|
|
#' @importFrom tidyr all_of
|
|
#' @importFrom tidyr ends_with
|
|
#'
|
|
#' @export
|
|
#'
|
|
#' @examples
|
|
#' index_plot(stRoke::score[score$event=="A",])
|
|
index_plot <- function(ds,id="id",sub_plot="_is",
|
|
scores=c("_is","_lo","_up","_per"),
|
|
dom_names=c("immediate","visuospatial","verbal",
|
|
"attention","delayed","total"),
|
|
facet.by=NULL){
|
|
|
|
if (length(facet.by)>1){stop("facet.by can be NULL or of length 1 only.")}
|
|
|
|
df_plot<-ds|>
|
|
dplyr::select(c(id,
|
|
facet.by,
|
|
tidyr::ends_with(scores)))|>
|
|
tidyr::pivot_longer(cols=-c(id,tidyr::all_of(facet.by)))|>
|
|
subset(grepl(sub_plot,name))|>
|
|
dplyr::mutate(value=as.numeric(value),
|
|
name=factor(name,labels = dom_names))
|
|
|
|
if (!is.null(facet.by)){
|
|
colnames(df_plot)<-c("id","facet","name","value")
|
|
} else {
|
|
colnames(df_plot)<-c("id","name","value")
|
|
}
|
|
|
|
if (sub_plot=="_is"){
|
|
index_plot<-df_plot|>
|
|
ggplot2::ggplot(mapping = ggplot2::aes(x=name, y=value, color=factor(id),
|
|
group=factor(id))) +
|
|
ggplot2::geom_point() +
|
|
ggplot2::geom_path() +
|
|
ggplot2::expand_limits(y=c(40,160)) +
|
|
ggplot2::scale_y_continuous(breaks=seq(40,160,by=10)) +
|
|
ggplot2::ylab("Index Score") +
|
|
ggplot2::xlab("Domain")+
|
|
ggplot2::labs(colour = "ID")
|
|
}
|
|
|
|
if (sub_plot=="_per"){
|
|
index_plot<-df_plot|>
|
|
ggplot2::ggplot(mapping = ggplot2::aes(x=name, y=value,
|
|
fill=factor(id)))+
|
|
ggplot2::geom_col(position = "dodge") +
|
|
ggplot2::expand_limits(y=c(0,100)) +
|
|
ggplot2::scale_y_continuous(breaks=seq(0,100,by=10)) +
|
|
ggplot2::xlab("Cognitive domains") +
|
|
ggplot2::ylab("Percentile") +
|
|
ggplot2::labs(fill = "ID")
|
|
}
|
|
|
|
if (!is.null(facet.by)){
|
|
index_plot + facet_grid(cols=vars(facet)) +
|
|
ggplot2::theme(axis.text.x = element_text(angle = 90,
|
|
vjust = 0.5, hjust=1))
|
|
|
|
} else {
|
|
index_plot
|
|
}
|
|
|
|
}
|
|
|