---
title: "TCR Demo Report"
output:
  rmdformats::material:
    self_contained: false
    fig_width: 8
    fig_height: 6.5
    mainfont: Arial,Helvetica,sans-serif
    fontfamily: Arial,Helvetica,sans-serif
---

```{r knitr-options, include=FALSE}

knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE,
               dpi = 250, fig.width = 20, fig.height = 8,
               dev.args = list( family = "Arial" ))

```

```{r report-path, include=FALSE}
# NOTE: The report_path name MUST match the name of the Rmd file
# e.g. MyReport.Rmd: report_path <- reportPath("MyReport")
library(NanoStringTCR)
library(DT)
report_path <- reportPath("TCR_DemoData")
```

```{r}

extrafont::loadfonts( device = "postscript" , quiet = TRUE )

# Load Data from Files - Change the below to your directory
data_dir <- file.path("/home", "rstudio", "NAS_data", "kgorman", "TCR_Projects", "DemoData")


rccs <- dir(file.path(data_dir, "RCCs"), pattern = "*\\.RCC$", full.names = TRUE)
rlf <- NULL#file.path(data_dir, "NS_Hs_CART_v1.0.rlf")
pheno <- file.path(data_dir, "sample_annot.csv")

```

```{r}

###############################
#### Configuration Section ####
###############################

# Set background threshold
thres <- 30

# Set Normalization Options (etiher or)
constantNormalize <- FALSE
cd3Normalize <- FALSE

# Set Time Dependent Options (etiher or)
includeTimeDependentVariable <- FALSE
timeSeriesVariable <- NULL

# Boxplot Configuration
firstBoxplotVariables <- c("Type", "Type")
secondBoxplotVariables <- NULL#c("Treatment", "Treatment")
thirdBoxplotVariables <- NULL#c("BatchCode", "BatchCode")

# Bargraph Configuration
colorBargraphBy <- "Type"
```

```{r report-template, include=FALSE}
report_template <- system.file("templates", "TCRAnalysisContent.Rmd", package = "NanoStringTCR")
```

```{r child=report_template}
```
