This function visualizes the regulatory network between gene modules as a heatmap, where each cell represents the regulatory score between a source and target module. The heatmap can display either positive, negative, or delta (positive minus negative) regulatory scores. Optionally, a dendrogram can be plotted to cluster modules based on their regulatory interactions.
Usage
ModuleRegulatoryHeatmap(
seurat_obj,
feature = "delta",
TFs_only = TRUE,
dendrogram = TRUE,
coord_fixed = TRUE,
max_val = 1,
min_val_label = 3,
high_color = "orange2",
mid_color = "white",
low_color = "dodgerblue",
wgcna_name = NULL
)Arguments
- seurat_obj
A Seurat object containing single-cell data and WGCNA results.
- feature
A character string specifying the type of regulatory score to plot. Options are 'positive' (positive regulatory score), 'negative' (negative regulatory score), or 'delta' (difference between positive and negative scores). Default is 'delta'.
- TFs_only
Logical; if TRUE (default), only transcription factor (TF) genes are included in the heatmap. If FALSE, all genes are considered in the regulatory network.
- dendrogram
Logical; if TRUE (default), a dendrogram is added to the heatmap to cluster modules based on their regulatory interactions. Default is TRUE.
- coord_fixed
Logical; if TRUE (default), aspect ratio in x and y axes are equal. Default is TRUE.
- max_val
Numeric; sets the maximum absolute value for the regulatory score. Any values exceeding this threshold are capped. Default is 1.
- min_val_label
Numeric; the minimum number of interactions required for a label to be displayed on a heatmap cell. Default is 3.
- high_color
Character string; the color representing high regulatory scores in the heatmap. Default is 'orange2'.
- mid_color
Character string; the color representing intermediate regulatory scores in the heatmap. Default is 'white'.
- low_color
Character string; the color representing low regulatory scores in the heatmap. Default is 'dodgerblue'.
- wgcna_name
The name of the hdWGCNA experiment in the seurat_obj@misc slot
Value
A ggplot2 object visualizing the module regulatory network as a heatmap, which can be
further customized or displayed using plot().
Details
The function visualizes the regulatory network between gene modules by plotting regulatory scores as a heatmap. Each cell in the heatmap represents the regulatory interaction between a source module (columns) and a target module (rows). The color of the cell represents the magnitude and direction (positive or negative) of the regulatory score. Users can choose to plot positive, negative, or delta scores and can adjust the color gradient and score thresholds. A dendrogram can be added to cluster modules based on their regulatory patterns, and labels can be shown for cells with a sufficient number of interactions.