tcr_plots.Rmd

---
title: "tcr_plots"
author: "Matthew Salaciak"
date: "12/8/2020"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```


```{r pressure, echo=FALSE}

tct.list <- c(tp1_tcr,tp2_tcr,tp3_tcr,tp4_tcr,tp5_tcr,tp6_tcr)
cell.list <- c("CD8 Exhausted","CD8 Teff","CD8 TEM"," CD8 t-cell 1","CD8 t-cell 2","CD8 t-cell 3","CD4 TCM","CD4 Naive", "CD4 Treg")




  for(k in 1:9) {
for (i in 1:6) {
  for (j in 1:6) {
      if(i<=j) {
        CloneTrack(tct.list[[i]],tct.list[[j]],cell.list[[k]], TRUE,TRUE,paste("Timepoint ", i, "vs", j,cell.list[[k]])) 
      }
    
  }
}
  }


rm(tct.list)


```


``` {r test}

View(FindTimePoint2.5(cluster17.avgLOG_timepoint,cluster17.markers))



```