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