fig4.Rmd

---
title: "Relasped mulitome"
output: html_notebook
editor_options: 
  chunk_output_type: console
---


```{r, warning=FALSE, message=FALSE, warning=FALSE, echo=F}
graphics.off()
rm(list=ls())
knitr::opts_chunk$set(fig.width=8, fig.height=6,dpi=300,
                      echo=FALSE, warning=FALSE, message=FALSE)
setwd("/fh/fast/furlan_s/user/owalt/exhaustion/relapse")
RES_DIR  <- file.path("res")     # SPECIFY HERE
RMD_DIR  <- file.path("rmd")     # SPECIFY HERE
FIG_DIR <- file.path("figs")

suppressPackageStartupMessages({
  library(monocle3)
  library(m3addon)
  library(reticulate)
  library(viridis)
  library(openxlsx)  
  library(dplyr)
  library(Matrix)
  library(ggplot2)
  library(xfun)
  library(pals)
  library(RColorBrewer)
  library(Signac)
  library(Seurat)
  library(ggplot2)
  library(future)
  library(GenomicRanges)
  library(EnsDb.Mmusculus.v79)
  library(ComplexHeatmap)
  library(BSgenome.Mmusculus.UCSC.mm10)
  #library(JASPAR2020)
  library(TFBSTools)
  library(patchwork)
  library(stringr)
  library(ggrepel)
  library(ggsignif)
  library(ggpubr)
  library(ArchR)
  library(harmony)
  library(viridis)
  library(scCustomize)
  library(SeuratDisk)
  library(BuenColors)
  library(pbmcapply)
  library(ggrastr)
  library(msigdbr)
  library(FigR)
  library(parallel)
})

set.seed(1234)
rel<- loadArchRProject("/fh/fast/furlan_s/user/owalt/exhaustion/relapse")
seu<-readRDS(file = "/fh/fast/furlan_s/user/owalt/exhaustion/relapse/relapse_seurat.rds")
```

configure python environment
```{r}
library(reticulate)
# /home/owaltner/mypython/bin/python

Sys.setenv(RETICULATE_PYTHON="/home/owaltner/mypython/bin/python")
use_virtualenv("/home/owaltner/mypython")
use_python("/home/owaltner/mypython/bin/python")
py_config()


Sys.setenv(PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION="python")
```

configure R environment
```{r, warning=FALSE, message=FALSE, warning=FALSE, echo=F}
dyn.load('/app/software/ArrayFire/3.8.1/lib64/libaf.so.3')
library(RcppArrayFire)
library(viewmaster)

Sys.setenv(MODULEPATH="/app/modules/all", MODULEPATH_ROOT="/app/modules/all", MODULESHOME="/app/lmod/lmod")
source("/app/lmod/lmod/init/R", echo=FALSE, max=Inf)
module("load", "MACS2/2.2.6-foss-2019b-Python-3.7.4")
module("load", "GCCcore/11.2.0")

#make cairo functional
knitr::opts_chunk$set(dev="CairoPNG")

detach("package:ArchR", unload=TRUE)
library(ArchR)

```

```{r colors}
rna_cols <- paletteContinuous(n=8)[c(1:3, 6:8)]
atac_cols <- paletteContinuous(set = "blueYellow")

pal<- rev(mako(n=9))
pal<-pal[1:8]
pal<-c("#ffffff", pal)
chromvar_cols<-pal

adt_cols <- paletteContinuous(set = "whiteBlue")
pseudotime_cols<- viridis::plasma(n=10)
tcr_cols <- c("gray90", rev(brewer.spectral(n =5)))

t <-BuenColors::jdb_palette("brewer_spectra")
multiome_cols <- c(t[2],t[3], "#e5e6e1", t[7],t[9])

h_cols <-rev(brewer.pal(name = "RdYlBu", n = 7))
rna_cols<-paletteContinuous(n=10)[c(1:4, 7:10)]
seu$cell_type%>% table()

seu$cell_type<-factor(seu$cell_type, levels = c("Tn", "Tcm", "Tem", "Tem_2", "Teff", "Tpex", "Tg_phex", "Tex", "Tex_cycling", "Ly6a-_Tex", "Ifng-_Tex"))

cell_type_cols<-c( "Ifng-_Tex" ="#191970","Ly6a-_Tex" = "#006400", "Tex" = "#87CEFA", "Tg_phex" = "#20B2AA","Tcm" = "#696969", "Teff" = "#9370DB", "Tem" = "#FF8C00", "Tem_2" = "#FF4500", "Tex_cycling" = "#1E90FF", "Tn" = "#ebeb78", "Tpex" ="#DC143C" )

cluster_cols<-c("0" = "#20B2AA","1" = "#006400", "8" = "#87CEFA", "10" ="#191970", "5" = "#696969", "2" = "#9370DB", "4" = "#FF8C00", "9" = "#FF4500", "6" = "#1E90FF", "3" = "#ebeb78", "7" ="#DC143C" )
```

#GSEA
```{r}
m_df<-msigdbr(species = "Mus musculus", category = "H")
oxphos<-m_df[m_df$gs_name == "HALLMARK_OXIDATIVE_PHOSPHORYLATION",]$gene_symbol
glyco<-m_df[m_df$gs_name == "HALLMARK_GLYCOLYSIS",]$gene_symbol

seu<-AddModuleScore(seu, features = list(oxphos), name = "oxphos")
seu<-AddModuleScore(seu, features = list(glyco), name = "glyco")

VlnPlot(seu, features = c("glyco1", "oxphos1"), group.by = "cell_type", cols = cell_type_cols, pt.size = 0)
FeaturePlot_scCustom(seu, features = c("glyco1", "oxphos1"), colors_use = rna_cols, max.cutoff = "q99", pt.size = 0.7, order =T )&NoAxes()
```