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#' A function to create a box and whisker plot by group ID
#'
#' A function to create a box and whisker plot by group ID.
#'
#'
#' @param data a (non-empty) matrix of data values
#' @param groups a (non-empty) vector of group IDs with length equal to the
#' number of rows in data
#' @param palette A color palette for plotting. The default is 'Paired.' See
#' colorbrewer2.org for alternatives.
#' @return Returns a box-whisker plot of the data by group ID.
#' @examples
#'
#' data(Nuclei)
#' data(Groups)
#' boxWhisker(Nuclei, Groups)
#'
#' #changing the color palette
#'
#' boxWhisker(data = Nuclei, groups = Groups, palette = 'Set1')
#'
#' @export boxWhisker
boxWhisker <- function(data, groups, palette = "Paired") {
dat <- as.matrix(data)
score <- matrix(dat, ncol = 1)
trait <- colnames(data)
trait <- rep(trait, each = nrow(dat))
group <- rep(groups, ncol(dat))
dat.df <- data.frame(score, trait, group)
dat.df$group <- factor(dat.df$group)
dat.trait <- factor(dat.df$trait)
p <- ggplot(dat.df, aes(trait, score))
p.save <- p + geom_boxplot(aes(fill = group), outlier.shape = NA) +
scale_fill_brewer(palette = palette) + theme(legend.position = "right",
legend.background = element_rect(fill = "#ffffffaa", colour = "black"),
panel.background = element_rect(fill = "white", colour = "black"),
axis.text.y = element_text(colour = "black", size = 15),
axis.text.x = element_text(colour = "black", size = 8),
axis.title = element_text(colour = "black", size = 15),
legend.key = element_rect(fill = "white "), panel.grid.minor = element_blank(),
panel.grid.major = element_blank())
return(p.save)
} #end FUNCTION
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