---

title: "Determine thresholds for protein expression"

author: Tobias Roider

date: "Last compiled on `r format(Sys.time(), '%d %B, %Y, %X')`"

output: 

  rmdformats::readthedown

editor_options: 

  chunk_output_type: console

---

```{r options, include=FALSE, warning = FALSE}

library(knitr)

opts_chunk$set(echo=TRUE, tidy=FALSE, include=TRUE, message=FALSE, cache.lazy = FALSE,

               dpi = 100, cache = FALSE, warning = FALSE, fig.height = 6.5)

opts_knit$set(root.dir = "../")

options(bitmapType = "cairo")

```

# Load packages and functions

```{r Load packages and functions}

library(Seurat)

library(tidyverse)

library(readxl)

library(ggpubr)

library(ggrastr)

source("R/Functions.R")

thresh <- list()

mytheme <- 

  theme_bw()+

  theme(panel.grid = element_blank())

```

# Read and handle data

```{r read data}

Combined_T <- readRDS("output/Tcells_Integrated.rds")

df <- readRDS("data/denoised_protein_totalVI.rds")

meta_protein <- readRDS("data/meta_protein_totalVI.rds")

df <- left_join(df, meta_protein %>% select(Barcode_full, log10_prot_size))

df <- df %>% left_join(., FetchData(Combined_T, vars=c("Barcode_full", "IdentI")), by="Barcode_full")

colnames(df) <- gsub(colnames(df), pattern = "_TotalA", replacement = "")

df <- filter(df, !is.na(IdentI))

df <- sample_frac(df, 0.25)

```

# Marker

## CD2

```{r}

thresh_tmp <- 75

epitope <- "CD2"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=700, y=4, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD2 <- thresh_tmp

```

## CD3

```{r}

thresh_tmp <- 75

epitope <- "CD3"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=500, y=4, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD3 <- thresh_tmp

```

## CD4

```{r}

thresh_tmp <- 90

epitope <- "CD4"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=500, y=4, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD4 <- thresh_tmp

```

## CD5

```{r}

thresh_tmp <- 125

epitope <- "CD5"

df_tmp <- df %>% 

   drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=700, y=4, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD5 <- thresh_tmp

```

## CD7

```{r}

thresh_tmp <- 100

epitope <- "CD7"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=750, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 1000)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD7 <- thresh_tmp

```

## CD8a

```{r}

thresh_tmp <- 35

epitope <- "CD8a"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=200, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 250)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD8a <- thresh_tmp

```

## CD10

```{r}

thresh_tmp <- 15

epitope <- "CD10"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.35, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=65, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 75)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD10 <- thresh_tmp

```

## CD103

```{r}

thresh_tmp <- 10

epitope <- "CD103"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=50, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 75)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD103 <- thresh_tmp

```

## CD11b

```{r}

thresh_tmp <- 15

epitope <- "CD11b"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 100)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD11b <- thresh_tmp

```

## CD11c

```{r}

thresh_tmp <- 40

epitope <- "CD11c"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 100)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD11c <- thresh_tmp

```

## CD127

```{r}

thresh_tmp <- 35

epitope <- "CD127"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 150)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD127 <- thresh_tmp

```

## CD134

```{r}

thresh_tmp <- 22.5

epitope <- "CD134"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 120)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD134 <- thresh_tmp

```

## CD137

```{r}

thresh_tmp <- 12.5

epitope <- "CD137"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 120)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD137 <- thresh_tmp

```

## CD150

```{r}

thresh_tmp <- 20

epitope <- "CD150"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 70)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD150 <- thresh_tmp

```

## CD152

```{r}

thresh_tmp <- 10

epitope <- "CD152"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 40)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD152 <- thresh_tmp

```

## CD16

```{r}

thresh_tmp <- 15

epitope <- "CD16"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 70)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD16 <- thresh_tmp

```

## CD161

```{r}

thresh_tmp <- 10

epitope <- "CD161"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.2, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=30, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 50)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD161 <- thresh_tmp

```

## CD183

```{r}

thresh_tmp <- 15

epitope <- "CD183"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.4, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 85)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD183 <- thresh_tmp

```

## CD184

```{r}

thresh_tmp <- 7.5

epitope <- "CD184"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 85)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD184 <- thresh_tmp

```

## CD185

```{r}

thresh_tmp <- 20

epitope <- "CD185"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.4, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=60, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 70)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD185 <- thresh_tmp

```

## CD19

```{r}

thresh_tmp <- 25

epitope <- "CD19"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 70)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD19 <- thresh_tmp

```

## CD194

```{r}

thresh_tmp <- 15

epitope <- "CD194"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=50, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 70)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD194 <- thresh_tmp

```

## CD195

```{r}

thresh_tmp <- 5

epitope <- "CD195"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 50)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD195 <- thresh_tmp

```

## CD197

```{r}

thresh_tmp <- 7.5

epitope <- "CD197"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=25, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 30)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD197 <- thresh_tmp

```

## CD20

```{r}

thresh_tmp <- 35

epitope <- "CD20"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=50, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 100)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD20 <- thresh_tmp

```

## CD21

```{r}

thresh_tmp <- 40

epitope <- "CD21"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 100)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD21 <- thresh_tmp

```

## CD22

```{r}

thresh_tmp <- 30

epitope <- "CD22"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 70)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD22 <- thresh_tmp

```

## CD223

```{r}

thresh_tmp <- 7.5

epitope <- "CD223"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=40, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 50)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD223 <- thresh_tmp

```

## CD23

```{r}

thresh_tmp <- 20

df %>% 

  #drop_na() %>%

  ggplot(aes(x=CD23, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 75)+

  mytheme

thresh$CD23 <- thresh_tmp

```

## CD24

```{r}

thresh_tmp <- 20

df %>% 

  ggplot(aes(x=CD24, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 75)+

  mytheme

thresh$CD24 <- thresh_tmp

```

## CD244

```{r}

thresh_tmp <- 30

epitope <- "CD244"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=75, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 200)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD244 <- thresh_tmp

```

## CD25

```{r}

thresh_tmp <- 75

epitope <- "CD25"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=200, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 400)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD25 <- thresh_tmp

```

## CD27

```{r}

thresh_tmp <- 150

epitope <- "CD27"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=500, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 750)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD27 <- thresh_tmp

```

## CD273

```{r}

thresh_tmp <- 15

df %>% 

  #drop_na() %>%

  ggplot(aes(x=CD273, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  ##xlim(0, 200)+

  mytheme

thresh$CD273 <- thresh_tmp

```

## CD274

```{r}

thresh_tmp <- 15

df %>% 

  #drop_na() %>%

  ggplot(aes(x=CD274, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 50)+

  mytheme

thresh$CD274 <- thresh_tmp

```

## CD279

```{r}

thresh_tmp <- 110

epitope <- "CD279"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.4)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=750, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 1300)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD279 <- thresh_tmp

```

## CD278

```{r}

thresh_tmp <- 200

df %>% 

  drop_na() %>%

  ggplot(aes(x=CD278, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 1000)+

  mytheme

thresh$CD278 <- thresh_tmp

```

## CD28

```{r}

thresh_tmp <- 30

df %>% 

  #drop_na() %>%

  ggplot(aes(x=CD28, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 200)+

  mytheme

thresh$CD28 <- thresh_tmp

```

## CD29

```{r}

thresh_tmp <- 60

df %>% 

  drop_na() %>%

  ggplot(aes(x=CD29, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 200)+

  mytheme

thresh$CD29 <- thresh_tmp

```

## CD31

```{r}

thresh_tmp <- 100

df %>% 

  drop_na() %>%

  ggplot(aes(x=CD31, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 200)+

  mytheme

thresh$CD31 <- thresh_tmp

```

## CD32

```{r}

thresh_tmp <- 20

df %>% 

  drop_na() %>%

  ggplot(aes(x=CD32, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 50)+

  mytheme

thresh$CD32 <- thresh_tmp

```

## CD357

```{r}

thresh_tmp <- 7.5

df %>% 

  drop_na() %>%

  ggplot(aes(x=CD357, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 50)+

  mytheme

thresh$CD357 <- thresh_tmp

```

## CD366

```{r}

thresh_tmp <- 20

epitope <- "CD366"

df_tmp <- df %>% 

  drop_na() %>% 

  mutate(isPos=!!sym(epitope)>thresh_tmp) %>% 

  add_prop(keep.n = F, vars = c("IdentI", "isPos"), group.vars = 1) %>% 

  filter(isPos==T) 

df %>% 

  drop_na() %>% 

  ggplot(aes(x=!!sym(epitope), y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, size=0.25, raster.dpi=300)+

  geom_text(data=df_tmp, inherit.aes = F, aes(x=60, y=3, label=round(Prop, 2)))+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  xlim(0, 75)+

  facet_wrap(~IdentI)+

  mytheme

thresh$CD366 <- thresh_tmp

```

## CD38

```{r}

thresh_tmp <- 50

df %>% 

  drop_na() %>%

  ggplot(aes(x=CD38, y=log10_prot_size))+

  geom_point_rast(shape=1, stroke=0.1, shape=1, stroke=0.1, size=0.25, alpha=0.25, raster.dpi=300)+

  geom_vline(xintercept = thresh_tmp, size=0.25, linetype="dashed")+

  facet_wrap(~IdentI)+

  xlim(0, 150)+

  mytheme

thresh$CD38 <- thresh_tmp

```

## CD39

```{r}