plot.correlation.heatmap — plot.correlation.heatmap • DEprot

Function to generate a correlation heatmap. Includes dendrogram and clustering of the data.

# S3 method for class 'correlation.heatmap'
plot(
  DEprot.object,
  correlation.method = "pearson",
  sample.subset = NULL,
  which.data = "imputed",
  palette = viridis::mako(100, direction = -1),
  correlation.scale.limits = c(0, 1),
  exclude.diagonal = FALSE,
  dendrogram.position = "left",
  dendrogram.color = "black",
  dendrogram.linewidth = 0.5,
  display.values = TRUE,
  values.color = NULL,
  values.decimals = 2,
  values.font.size = 2,
  values.transparency = 1,
  plot.title = paste0("**", stringr::str_to_title(correlation.method), " correlation**"),
  plot.subtitle = NULL,
  clustering.method = "complete"
)

Arguments

DEprot.object: An object of class DEprot.
correlation.method: String indicating the clustering method to use to generate the correlation matrix. Possible options: 'pearson', 'spearman', 'kendall'. Default: "pearson".
sample.subset: Vector indicating the name of the columns (column.id in the metadata table) to use/subset for the correlation. Default: NULL (no subsetting).
which.data: String indicating which type of counts should be used. One among: 'raw', 'normalized', 'norm', 'imputed', 'imp'. Default: "imputed".
palette: Vector of colors corresponding to the palette to use for the heatmap color scale. Default: viridis::mako(100, direction = -1).
correlation.scale.limits: Two-elements vector to indicate lower and higher limits, respectively, to apply to the correlation coefficient color scale. Default: c(0,1).
dendrogram.position: String indicating the position of the dendrogram. One among: "top", "bottom", "left", "right". Default: "left".
dendrogram.color: String indicating the color of the dendrogram lines. Default: "black".
dendrogram.linewidth: Numeric value indicating the line.width of the dendrogram. Default: "black".
display.values: Logical value indicating whether the correlation coefficient should be displayed for each cell. Default: TRUE.
values.color: String indicating the color to use for the correlation coefficient labels. Default: "NULL": colors will be assigned automatically depending on the background contrast, white for dark colors and black for light ones.
values.decimals: Numeric value indicating the number of decimals at which round the correlation coefficient labels. Default: 2.
values.font.size: Numeric value indicating the font size of the correlation coefficient labels. Default: 2.
values.transparency: Numeric value between 0-1 indicating the transparency (alpha) of the correlation coefficient labels. Default: 1, full color.
plot.title: String indicating the main title of the plot. Default: paste(stringr::str_to_title(correlation.method), "correlation").
plot.subtitle: String indicating the subtitle of the plot. Default: NULL.
clustering.method: String indicating the clustering method to use. The value should be (an unambiguous abbreviation of) one among: 'ward.D', 'ward.D2', 'single', 'complete', 'average' (= UPGMA), 'mcquitty' (= WPGMA), 'median' (= WPGMC) or 'centroid' (= UPGMC).

Value

A DEprot.correlation with the correlation heatmap in ggplot format.