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updated CSMF5 plot with option to return barplot created by ggplot
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@jarathomas
jarathomas committed Apr 16, 2021
1 parent fca949c commit 8dd2dd3
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2 changes: 1 addition & 1 deletion InterVA5_1.0/DESCRIPTION
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Expand Up @@ -2,7 +2,7 @@ Package: InterVA5
Type: Package
Title: Replicate and Analyse 'InterVA5'
Version: 1.1.2
Date: 2020-11-13
Date: 2021-04-16
Authors@R: c(
person("Matthew", "Boyas", role = "aut"),
person("Peter", "Byass", role = "aut"),
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111 changes: 69 additions & 42 deletions InterVA5_1.0/R/InterVA5.plot.R
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Expand Up @@ -182,11 +182,14 @@ COMCAT.interVA5 <- function(va){
#' goes into an extra category "Undetermined". Default set to "FALSE".
#' @param noplot A logical value indicating whether the plot will be shown. If
#' it is set to "TRUE", only the CSMF will be returned.
#' @param title A character string for the title of the CSMF plot.
#' @param top.plot the maximum number of causes to plot in bar plot
#' @param min.prob The minimum probability that is to be plotted in bar chart,
#' or to be labeled in pie chart.
#' @param type An indicator of the type of chart to plot. "pie" for pie chart;
#' "bar" for bar chart.
#' @param return.barplot A logical indicating if the (barplot) ggplot() object
#' should be returned (instead of printed). Default value is FALSE.
#' @param ... Arguments to be passed to/from graphic function
#' \code{\link[graphics]{barplot}}, \code{\link[graphics]{pie}}, and more
#' graphical paramters (see \code{\link[graphics]{par}}). They will affect the
Expand Down Expand Up @@ -216,20 +219,22 @@ COMCAT.interVA5 <- function(va){
#'
#' ## Population level summary using pie chart
#' CSMF.summary2 <- CSMF5(sample.output, type = "pie",
#' min.prob = 0.01, main = "population COD distribution using pie chart",
#' min.prob = 0.01, title = "population COD distribution using pie chart",
#' clockwise = FALSE, radius = 0.7, cex = 0.7, cex.main = 0.8)
#'
#' ## Population level summary using bar chart
#' CSMF.summary3 <- CSMF5(sample.output, type = "bar",
#' min.prob = 0.01, main = "population COD distribution using bar chart",
#' min.prob = 0.01, title = "population COD distribution using bar chart",
#' cex.main = 1)
## Population level summary specified by number of top causes
#' CSMF.summary4 <- CSMF5(sample.output, type = "bar",
#' top.plot = 5, main = "Top 5 population COD distribution",
#' top.plot = 5, title = "Top 5 population COD distribution",
#' cex.main = 1)
#' }
#'
CSMF5 <- function (va, top.aggregate = NULL, InterVA.rule = FALSE, noplot = FALSE, type="bar", top.plot = 10, min.prob = 0, ... ) {
CSMF5 <- function (va, top.aggregate = NULL, InterVA.rule = FALSE, noplot = FALSE,
title = "Top CSMF Distribution", type = "bar", top.plot = 10,
return.barplot = FALSE, min.prob = 0, ... ) {

## Check if there is a valid va object
if (class(va) == "interVA5") {
Expand Down Expand Up @@ -331,30 +336,45 @@ CSMF5 <- function (va, top.aggregate = NULL, InterVA.rule = FALSE, noplot = FALS
pie.color <- grey.colors(length(dist.cod.sort[dist.cod.sort >= min.prob]))
pie.color.left <- rep(pie.color[length(pie.color)], length(dist.cod.sort[dist.cod.sort < min.prob]))
pie.color <- c(pie.color, pie.color.left)
pie(dist.cod.sort, col = pie.color,labels = names(dist.cod.sort)[dist.cod.sort > min.prob], ...)
pie(dist.cod.sort, main = title,
col = pie.color, labels = names(dist.cod.sort)[dist.cod.sort > min.prob],
...)
}
## Make bar plot upon request
if (type == "bar") {
## dist.cod.min <- dist.cod[dist.cod >= min.prob ]
dist.cod.min <- dist.cod[dist.cod > min.prob ]
dist.cod.min <- sort(dist.cod.min, decreasing = FALSE)
par(las = 2)
par(mar = c(5,15,4,2))
if (requireNamespace("ggplot2", quietly = TRUE)) {
barplot.df <- data.frame(Probability = dist.cod.min, Causes = names(dist.cod.min))
barplot.df <- data.frame(Probability = dist.cod.min,
Causes = names(dist.cod.min))
g <- ggplot2::ggplot(barplot.df,
ggplot2::aes(x = stats::reorder(Causes, seq(1:length(Causes))),
y = Probability,
fill = stats::reorder(Causes, seq(1:length(Causes))))) +
ggplot2::geom_bar(stat="identity") + ggplot2::xlab("") + ggplot2::ylab("")
g <- g + ggplot2::coord_flip() +
ggplot2::scale_fill_grey(start = 0.8, end = 0.2) +
ggplot2::theme(legend.position = "none")
print(g)
ggplot2::aes(x = stats::reorder(Causes,
seq(1:length(Causes))),
y = Probability,
fill = stats::reorder(Causes,
seq(1:length(Causes))))) +
ggplot2::geom_bar(stat="identity") +
ggplot2::xlab("") +
ggplot2::ylab("") +
ggplot2::coord_flip() +
ggplot2::scale_fill_grey(start = 0.8, end = 0.2) +
ggplot2::ggtitle(title) +
ggplot2::theme(legend.position = "none")
if (return.barplot) {
return(g)
} else {
par(las = 2)
par(mar = c(5,15,4,2))
print(g)
}

} else {
bar.color <- grey.colors(length(dist.cod.min))
bar.color <- rev(bar.color)
barplot(dist.cod.min, horiz = TRUE, names.arg = names(dist.cod.min), col = bar.color, cex.names=0.8, xlab = "Probability", ...)
barplot(dist.cod.min, horiz = TRUE, names.arg = names(dist.cod.min),
main = title, col = bar.color, cex.names=0.8,
xlab = "Probability", ...)
}
}
## Save the population distribution
Expand All @@ -372,13 +392,14 @@ CSMF5 <- function (va, top.aggregate = NULL, InterVA.rule = FALSE, noplot = FALS
#' or to be labeled in pie chart.
#' @param type An indicator of the type of chart to plot. "pie" for pie chart;
#' "bar" for bar chart.
#' @param title A character string for the title of the CSMF plot.
#' @param ... Arguments to be passed to/from graphic function
#' \code{\link[graphics]{barplot}}, \code{\link[graphics]{pie}}, and more
#' graphical paramters (see \code{\link[graphics]{par}}). They will affect the
#' main title, size and font of labels, and the radius of the pie chart.
#' @seealso \code{\link{CSMF5}}
#' @keywords InterVA
#' @export InterVA5.plot
#' @keywords InterVA
#' @examples
#'
#' \dontrun{
Expand All @@ -399,13 +420,13 @@ CSMF5 <- function (va, top.aggregate = NULL, InterVA.rule = FALSE, noplot = FALS
#' main = "2nd sample VA analysis using bar chart", cex.main = 0.8)
#' }
#'
InterVA5.plot <- function(va, type="bar", min.prob = 0.01, ... ){
InterVA5.plot <- function(va, type = "bar", title = "Top CSMF Distribution", min.prob = 0.01, ... ){

# for future compatibility with non-standard input
if(!is.null(va$wholeprob)){
if (!is.null(va$wholeprob)) {
causenames <- names(va$wholeprob)
causeindex <- 1:length(causenames)
}else{
} else {
cat("Cause of death undetermined for this case\n")
return()
}
Expand All @@ -420,49 +441,55 @@ InterVA5.plot <- function(va, type="bar", min.prob = 0.01, ... ){


## Check if there is a valid va object
if(length(va) < 1){
cat("No va object found")
return()
}
if (length(va) < 1) {
cat("No va object found")
return()
}
## Find the probability distribution
dist <- unlist(va[15])
dist <- unlist(va[15])
dist.cod <- dist[causeindex]/sum(dist[causeindex])
## Check if there is CODs above the minimum cut-off for prob
if(max(dist.cod) < min.prob){
if (max(dist.cod) < min.prob) {
cat("No COD larger than the minimum probability cut off line")
return()
}
names(dist.cod)<-causenames
names(dist.cod) <- causenames
## Make pie plot upon request
if( type == "pie" ){
if (type == "pie") {
dist.cod.sort <- sort(dist.cod, decreasing=TRUE)
pie.color <- grey.colors(length(dist.cod.sort[dist.cod.sort >= min.prob]))
pie.color.left <- rep(pie.color[length(pie.color)], length(dist.cod.sort[dist.cod.sort < min.prob]))
pie.color <- c(pie.color, pie.color.left)
pie(dist.cod.sort, col = pie.color,labels = names(dist.cod.sort)[dist.cod.sort > min.prob], ...)

pie(dist.cod.sort, main = title, col = pie.color,labels = names(dist.cod.sort)[dist.cod.sort > min.prob], ...)
}
## Make bar plot upon request
if( type == "bar"){
dist.cod.min <- dist.cod[dist.cod >= min.prob ]
if (type == "bar") {
dist.cod.min <- dist.cod[dist.cod >= min.prob]
dist.cod.min <- sort(dist.cod.min, decreasing = FALSE)
par(las = 2)
par(mar = c(5,15,4,2))
if (requireNamespace("ggplot2", quietly = TRUE)) {
barplot.df <- data.frame(Probability = dist.cod.min, Causes = names(dist.cod.min))
barplot.df <- data.frame(Probability = dist.cod.min,
Causes = names(dist.cod.min))
g <- ggplot2::ggplot(barplot.df,
ggplot2::aes(x = stats::reorder(Causes, seq(1:length(Causes))),
y = Probability,
fill = stats::reorder(Causes, seq(1:length(Causes))))) +
ggplot2::geom_bar(stat="identity") + ggplot2::xlab("") + ggplot2::ylab("")
g <- g + ggplot2::coord_flip() +
ggplot2::scale_fill_grey(start = 0.8, end = 0.2) +
ggplot2::theme(legend.position = "none")
ggplot2::aes(x = stats::reorder(Causes,
seq(1:length(Causes))),
y = Probability,
fill = stats::reorder(Causes,
seq(1:length(Causes))))) +
ggplot2::geom_bar(stat="identity") +
ggplot2::xlab("") + ggplot2::ylab("") +
ggplot2::coord_flip() +
ggplot2::scale_fill_grey(start = 0.8, end = 0.2) +
ggplot2::ggtitle(title) +
ggplot2::theme(legend.position = "none")
print(g)
} else {
bar.color <- grey.colors(length(dist.cod.min))
bar.color <- rev(bar.color)
barplot(dist.cod.min, horiz = TRUE, names.arg = names(dist.cod.min), col = bar.color, cex.names=0.8, xlab = "Probability", ...)
barplot(dist.cod.min, horiz = TRUE, names.arg = names(dist.cod.min),
main = title, col = bar.color, cex.names=0.8,
xlab = "Probability", ...)
}
}
}
13 changes: 10 additions & 3 deletions InterVA5_1.0/man/CSMF5.Rd
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10 changes: 9 additions & 1 deletion InterVA5_1.0/man/InterVA5.plot.Rd
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