Factor_Motif_Plot {AnanseSeurat}

Factor_Motif_Plot

Description

plot both expression of a TF, and the motif accessibility of the associated motif. Finally, fetch the motif logo from the Maelstrom directory.

Usage

Factor_Motif_Plot(
  seurat_object,
  TF_list,
  assay_RNA = "RNA",
  assay_maelstrom = "MotifTFanticor",
  logo_dir = "~/maelstrom/logos",
  col = c("darkred", "white", "darkgrey"),
  dim_reduction = "umap"
)

Arguments

seurat_object

seurat object

TF_list

list of TFs to plot the expression and linked motif Z-score for

assay_RNA

RNA_count_assay assay containing the RNA data

assay_maelstrom

maelstrom assay used for zscore vizualization, often either TFcor or TFanticor

logo_dir

directory containing motif logos generated by gimme maelstrom

col

colours used for zscore vizualization

dim_reduction

dimensionality reduction method to use

Value

patchwork plot containing a expression dimreduction plot, a maelstrom motif score dimreduction plot, and a png image of the motif

Examples

sce_small <- readRDS(system.file("extdata","sce_small.Rds",package = 'AnanseSeurat'))
logos_dir_path <- system.file("extdata","maelstrom","logos",package = 'AnanseSeurat')
sce_small <- Factor_Motif_Plot(sce_small,
  c('gene1', 'gene2'),
  dim_reduction = 'pca',
  logo_dir = logos_dir_path)