################################################################################
### Load libraries ###
################################################################################

library(Seurat)
library(tidyverse)
library(sctransform)
library(DT)
library(scCustomize)
library(RColorBrewer)

################################################################################
### Define file paths ###
################################################################################

integrate_object_path <- "PATH_TO_SEURAT_OBJECT"

################################################################################
### Load data ###
################################################################################

integrated_seurat_object <- readRDS(file = integrate_object_path)

################################################################################
### Feature plot ###
################################################################################

DefaultAssay(integrated_seurat_object) <- "RNA"

pal <- c ("#ffffcc", "#ffeda0", "#fed976", "#feb24c", "#fd8d3c", "#fc4e2a", "#e31a1c", "#bd0026", "#800026")

#AGAP002914 - Galactokinase
FeaturePlot_scCustom(integrated_seurat_object,
                     features = "AGAP002914",
                     na_cutoff = 1,
                     order = TRUE,
                     pt.size = 0.4,
                     colors_use = pal,
                     na_color = "lightgray")+ 
  NoLegend() + 
  NoAxes()

#AGAP004017 - LRR8
FeaturePlot_scCustom(integrated_seurat_object,
                     features = "AGAP004017",
                     na_cutoff = 1,
                     pt.size = 0.4,
                     order = TRUE,
                     colors_use = pal,
                     na_color = "lightgray")+ 
  NoLegend() + 
  NoAxes()

#AGAP001899 - FAS
FeaturePlot_scCustom(integrated_seurat_object,
                     features = "AGAP001899",
                     na_cutoff = 1,
                     pt.size = 0.4,
                     order = TRUE,
                     colors_use = pal,
                     na_color = "lightgray")+ 
  NoLegend() + 
  NoAxes()

#AGAP00 - Rdl
FeaturePlot_scCustom(integrated_seurat_object,
                     features = "Rdl",
                     na_cutoff = 1,
                     pt.size = 0.4,
                     order = TRUE,
                     colors_use = pal,
                     na_color = "lightgray")+ 
  NoLegend() + 
  NoAxes()

#AGAP00 - CLIPB14
FeaturePlot_scCustom(integrated_seurat_object,
                     features = "CLIPB14",
                     na_cutoff = 1,
                     pt.size = 0.4,
                     order = TRUE,
                     colors_use = pal,
                     na_color = "lightgray")+ 
  NoLegend() + 
  NoAxes()

#AGAP010186 - Echinoid
FeaturePlot_scCustom(integrated_seurat_object,
                     features = "AGAP010186",
                     na_cutoff = 1,
                     pt.size = 0.4,
                     order = TRUE,
                     colors_use = pal,
                     na_color = "lightgray")+ 
  NoLegend() + 
  NoAxes()