This class facilitates the creation of 2D heatmaps for visualizing biological data, integrating significant levels and z-scores with customizable heatmap configurations.

This function initializes a MultifeatureGrid object with data and configuration for creating a multi-feature grid heatmap. It allows customization of the heatmap's title, axis labels, color palette, and more.

MultifeatureGrid(
  data,
  title = "Heatmap",
  x_label = "X Label",
  y_label = "Y Label",
  logpval_label = "-log10(p-value)",
  zscore_label = "Activation z-score",
  numitems_label = "Number of Genes",
  color_palette = "RdYlBu",
  breaks = seq(-1, 1, 0.5)
)

Arguments

data

A data.frame containing the data to be visualized in the heatmap. The data frame should have columns that match the expected metadata fields (e.g., significance values, z-scores).

title

The title of the heatmap. Default is "Heatmap".

x_label

The label for the x-axis. Default is "X Label".

y_label

The label for the y-axis. Default is "Y Label".

logpval_label

The label for the legend describing the -log10(p-value). Default is "-log10(p-value)".

zscore_label

The label for the legend describing the activation z-score. Default is "Activation z-score".

numitems_label

The label for the legend describing the number of genes or items. Default is "Number of Genes".

color_palette

The name of the color palette to use for the heatmap. Default is "RdYlBu". This should be a valid palette name recognized by RColorBrewer.

breaks

A numeric vector specifying the breakpoints for color mapping across the heatmap's values. Default is seq(-1, 1, 0.5).

Value

An object of class MultifeatureGrid initialized with the specified parameters.

Slots

data

A data frame containing heatmap data.

title

The title of the heatmap.

x_label

Label for the X-axis.

y_label

Label for the Y-axis.

logpval_label

Label for the legend of log10(p-value).

zscore_label

Label for the legend of z-scores.

numitems_label

Label for the legend describing the number of items (e.g., genes).

color_palette

The name of the RColorBrewer color palette to be used.

breaks

Numeric vector of breakpoints for color mapping.

Examples

data <- data.frame(
  tissue = factor(rep(c("Tissue1", "Tissue2"), each = 4)),
  signaling = factor(rep(c("Pathway1", "Pathway2", "Pathway3", "Pathway4"), 2)),
  Activation_z_score = runif(8, -2, 2),
  p = runif(8, 0, 0.05),
  number_of_genes = sample(1:100, 8)
)
mg <- MultifeatureGrid(data)
 library(MultiModalGraphics)
 data <- get_multifeature_grid_df()
 mg <- MultifeatureGrid(data)
 plot_heatmap(mg,  independantVariable = "tissue")
#> Warning: Removed 32 rows containing missing values or values outside the scale range
#> (`geom_point()`).