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