TFNetworkPlot: TFNetworkPlot
In smorabit/hdWGCNA: hdWGCNA

TFNetworkPlot

R Documentation

TFNetworkPlot

Description

Plots a network of TFs and predicted target genes.

Usage

TFNetworkPlot(
  seurat_obj,
  selected_tfs,
  depth = 2,
  edge_weight = "Cor",
  cutoff = 0.01,
  color_cutoff = 0.75,
  target_type = "both",
  use_regulons = TRUE,
  label_genes = NULL,
  label_TFs = 1,
  no_labels = FALSE,
  TFs_only = FALSE,
  high_color = "orange2",
  mid_color = "white",
  low_color = "dodgerblue",
  node_colors = c("black", "darkorchid4", "mediumpurple2"),
  wgcna_name = NULL
)

Arguments

`seurat_obj`	A Seurat object
`selected_tfs`	A list of TFs
`depth`	Number of layers to extend the TF network from the selected_tfs. For example, if depth=2 (default), the target genes of selected_tfs are shown, and additional target genes are shown for other TFs that are target genes of the original selected_tfs.
`edge_weight`	Attribute to use to color the network edges. "Cor" to show the pearson correlation, or "Gain" to show the importance score from the XGBoost model.
`cutoff`	Cutoff for the edge weights, links below this value will not be included.
`color_cutoff`	Maximum value for the colorscale for the edge weights.
`target_type`	Type of target genes to show in the network. "Positive" shows genes with expression positively correlated with selected_tfs, "Negative" shows genes that are negatively correlated, and "Both" shows both (default).
`use_regulons`	Logical indicating whether to use the TF-gene links defined in the TF Regulons (TRUE, default), or all putative TF-gene links (FALSE).
`label_genes`	List of target genes to label in the network plot.
`label_TFs`	The depth level in the network to plot the names of TFs.
`no_labels`	Logical indicating whether or not to remove all labels.
`TFs_only`	Logical indicating whether or not to use only TFs in the plot or to use TFs and other genes.
`high_color`	Color corresponding to positive edge weights
`mid_color`	Color corresponding to edge weights close to 0
`low_color`	Color corresponding to negative edge weights
`node_colors`	List of color names for the TFs and genes at each depth. For example, if depth=2, you should supply a list of 3 colors corresponding to the selected_tfs (depth 0), the primary target genes (depth 1), and the secondary target genes (depth 2).
`wgcna_name`	The name of the hdWGCNA experiment in the seurat_obj@misc slot