lecture-07-inclass.Rmd

```{r}
library(tidyverse)
library(readxl)
```


```{r}
chr16 <- read_tsv("~/Desktop/chr16_roi.tsv",
                  col_names = c("Chrom", 
                                "Start",
                                "End",
                                "Sequence",
                                "Count",
                                "Strand"))
```
```{r}
chr16 <- 
  chr16 |>
  mutate(Midpoint = (Start + End)/2)
```

```{r}
ggplot(chr16, aes(x = Midpoint, y = Count)) +
  geom_point() + 
  ylim(0,7)
```


```{r}
pileup <- function(start, end){
  coords <- c()
  for (i in 1:length(start)) {
      newcoords <- start[i]:end[i]
      coords <- c(coords, newcoords)
  }
  coords
}
```

```{r}
pileup(c(1, 3), c(5,8))
```
```{r}
pileup_coords <- pileup(chr16$Start, chr16$End)
```

```{r}
hist(pileup_coords, breaks = 400)
```

```{r}
pileup_df <- data_frame(coords = pileup_coords)
```

```{r}
ggplot(pileup_df, aes(x = coords)) + 
  geom_histogram(bins = 400) + 
  scale_y_continuous(trans = "log2") 
```

```{r}
library(readxl)
```


```{r}
ts4 <- read_excel(
  "~/Desktop/Nagalakshmi_etal_2008_from_TableS4.xls")
```


```{r}
ggplot(ts4,
       aes(x = SGD_Start, 
           y = Chrom, 
           width = SGD_End - SGD_Start + 1, 
           fill = Transcription_level_log2, 
           height=0.5)) + 

    scale_fill_distiller(palette="RdYlBu",
                         #direction=-1,
                         na.value = "white",
                         limits = c(0,10)) +
  geom_tile() + 
  theme_classic()

ggsave("expression-output.png", dpi=600)
```