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Update function_recursiveCorPlot.R #4

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30 changes: 18 additions & 12 deletions R/function_recursiveCorPlot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
#' @param caption caption (string) to be included
#' @return nothing, or h-clust object if return_h_object was set to TRUE
#' @export
recursiveCorPlot <- function(normalised_correlated_data, labels, font_scale , legend_scale , method="ward.D2", return_h_object = FALSE, caption=NULL) {
recursiveCorPlot <- function(normalised_correlated_data, labels, font_scale , legend_scale , method="ward.D2", signed = TRUE, return_h_object = FALSE, caption=NULL) {
col2 <- grDevices::colorRampPalette(c("#67001F", "#B2182B", "#D6604D", "#F4A582",
"#FDDBC7", "#FFFFFF", "#D1E5F0", "#92C5DE",
"#4393C3", "#2166AC", "#053061"))
Expand All @@ -44,6 +44,8 @@ recursiveCorPlot <- function(normalised_correlated_data, labels, font_scale , le
base::as.matrix() |>
base::t() |>
stats::cor()

plt <- if(signed == TRUE) plt else abs(plt)


# find order by taking correlation of the correlation
Expand Down Expand Up @@ -89,18 +91,14 @@ recursiveCorPlot <- function(normalised_correlated_data, labels, font_scale , le


p1 <- ggplot2::ggplot(plt.expanded2, ggplot2::aes(
x = .data$x.order,
y = .data$y.order,
radius = ((abs(.data$value) * 0.7) + 0.3) / 2 - 0.05,
# [0.3 , 0.8] + 0.2 smoothened from lwd/border
fill = .data$value,
col = .data$value,
label = .data$x
)
) +
x = .data$x.order,
y = .data$y.order,
radius = ((abs(.data$value) * 0.7) + 0.3) / 2 - 0.05,
# [0.3 , 0.8] + 0.2 smoothened from lwd/border
fill = .data$value,
col = .data$value,
label = .data$x)) +
ggplot2::geom_tile(col = "gray", fill = "white", lwd = 0.15) +
ggplot2::scale_fill_gradientn(colours = col2(200), na.value = "grey50", limits = c(-1, 1), guide = "none") + # guide = "colourbar",
ggplot2::scale_color_gradientn(colours = col2(200), na.value = "grey50", limits = c(-1, 1), guide = "none") +
geom_circle(radius.fixed = T) + # from THIS repo
ggplot2::scale_x_discrete(labels = NULL, breaks = NULL) +
ggplot2::theme(
Expand All @@ -116,6 +114,14 @@ recursiveCorPlot <- function(normalised_correlated_data, labels, font_scale , le
ggplot2::labs(y = NULL, x = NULL, main = NULL) +
ggplot2::coord_fixed() +
ggplot2::scale_y_continuous(name = NULL, breaks = base::length(o):1, labels = o)

p1 <- if (signed == T) {p1 +
ggplot2::scale_fill_gradientn(colours = col2(200), na.value = "grey50", limits = c(-1,1), guide = "none") + # guide = "colourbar",
ggplot2::scale_color_gradientn(colours = col2(200), na.value = "grey50", limits = c(-1,1), guide = "none")
} else {p1 +
ggplot2::scale_color_distiller(palette = "Spectral", na.value = "grey50", limits = c(0,1), guide = "none") + # guide = "colourbar",
ggplot2::scale_fill_distiller(palette = "Spectral", na.value = "grey50", limits = c(0,1), guide = "none")
}



Expand Down