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#' Heatmap Plot (Upper Triangle)
#'
#' Minimal ggplot2 relationship structure plot showing the upper triangle
#' in the top-right corner with no axis labels.
#' @param R A square numeric correlation matrix
#' @param title Optional plot title
#' @param labels Logical to plot column names or not (default FALSE)
#' @param order Optional character vector of the order you want the plot sorted in
#'
#' @return A ggplot object
#'
#' @examples
#' X <- matrix(data = rnorm(100), nrow = 10)
#' R <- cor(X)
#' heatmap(R, title = 'Example Correlation Plot')
#'
#' @importFrom reshape2 melt
#' @import ggplot2
#' @export
heatmap <- function(R, title = NULL, labels = FALSE, order = NULL){
R_list <- tryCatch({
if(is.matrix(R)){
Rm <- R
cnames <- colnames(Rm)
rnames <- rownames(Rm)
}else{
Rm <- as.matrix(R)
cnames <- colnames(Rm)
rnames <- rownames(Rm)
}
if(nrow(Rm) == ncol(Rm)){
if(!is.null(order)){
order <- get_order(Rm)
M <- Rm[order, order]
}
list(
M = M[upper.tri(M)],
cnames = cnames,
rnames = rnames,
p = ncol(M)
)
}else{
stop('Input must be coercible to a square matrix')
}
}, error = function(e){
stop(paste('Invalid input for heatmap:', e$message))
})
if(is.null(R_list$cnames)){
R_list$cnames <- as.character(seq_len(R_list$p))
}
if(is.null(R_list$rnames)){
R_list$rnames <- as.character(seq_len(R_list$p))
}
# Now get a df from the upper triangle
m <- length(R_list$R)
n <- as.integer((1 + sqrt(1 + 8 * m)) / 2)
M <- matrix(NA, n, n)
M[upper.tri(M)] <- R_list$R
colnames(M) <- R_list$cnames
rownames(M) <- R_list$rnames
df <- reshape2::melt(M, na.rm = TRUE)
colnames(df) <- c('i', 'j', 'value')
df$i <- as.numeric(df$i)
df$j <- as.numeric(df$j)
# And plot it
p <- ggplot2::ggplot(
data = df,
ggplot2::aes(x = .data$j, y = .data$i, fill = .data$value)
) +
ggplot2::geom_tile() +
ggplot2::scale_y_reverse() +
ggplot2::coord_fixed(clip = 'off') +
ggplot2::scale_fill_gradient2(
low = 'red',
mid = 'white',
high = 'blue',
midpoint = 0,
limits = c(-1, 1),
name = NULL,
guide = 'none'
) +
ggplot2::theme_void()
if(!is.null(title)){
p <- p +
ggplot2::ggtitle(title) +
ggplot2::theme(
plot.title = ggplot2::element_text(hjust = 0.5)
)
}
if(labels){
col_label_df <- data.frame(
j = seq_len(n)[-1],
i = 0,
label = R_list$cnames[-1]
)
row_label_df <- data.frame(
j = seq_len(n)[-n],
i = seq_len(n)[-n],
label = R_list$rnames[-n]
)
max_nchar <- max(nchar(R_list$cnames))
top_margin <- 5 + max_nchar * 2
p <- p +
ggplot2::geom_text(
data = col_label_df,
ggplot2::aes(x = .data$j, y = .data$i, label = .data$label),
inherit.aes = FALSE,
angle = 90,
hjust = 0,
vjust = 0.5
) +
ggplot2::geom_text(
data = row_label_df,
ggplot2::aes(x = .data$j, y = .data$i, label = .data$label),
inherit.aes = FALSE,
hjust = 1,
vjust = 0.5
) +
ggplot2::theme(
plot.margin = ggplot2::margin(
t = top_margin,
r = 5,
b = 5,
l = 5
)
)
}
return(p)
}
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