5abcd.Rmd

---
title: "Figure 5"
output:
  html_document:
    df_print: paged
---


```{r eval=TRUE, message=FALSE, warning=FALSE, include=TRUE}
suppressPackageStartupMessages(source("scripts/themes.R"))

```
```{r eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
tm.facs <- loadObject(filename = url("https://scfind.cog.sanger.ac.uk/indexes/tm_facs.rds"))
atac <- loadObject(filename = url("https://scfind.cog.sanger.ac.uk/indexes/atacseq.rds"))
```

## Figure 5a - This will generate .bed format file for the UCSC Genome Browser
```{r eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
source("scripts/6ac.R")
for( tissue in c("Heart", "Liver", "Spleen"))
{
    generateUCSCBedFileForEnhancers(atac, query.gene = "Nr4a1", 
                                    tissue = tissue, window = c(1e5, 0), 
                                    target.window = c("chr15", 101097277, 101105225 ), 
                                    annotation = loadAnnotation("data/fig6ac.tsv"))
}
```


## Figure 5b - This will generate .bed format file for the UCSC Genome Browser
```{r eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
for( tissue in c("Heart", "Liver", "Spleen"))
{
    generateUCSCBedFileForEnhancers(atac, query.gene = "Cd36", 
                                    tissue = tissue, window = c(1e5, 0), 
                                    target.window = c("chr5", 17188577, 17388756 ), 
                                    annotation = loadAnnotation("data/fig6ac.tsv"))
}
```


## Figure 5c
```{r, warning=FALSE}
df.6d <- read.table("data/fig6d.csv", sep = ",", header = T, stringsAsFactors = F)

p.6d <- ggplot(df.6d, aes(x=celltype, y=motif, fill=density)) + 
    theme_minimal() + theme(axis.title.y = element_blank(), axis.title.x = element_blank(), axis.text.x=element_text(hjust = 0, angle = -30),  text = element_text(size = 14), strip.text.x = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + 
    labs(fill = "Number of\nmotif/peak") +
    scale_fill_gradient2(high = colorRampPalette(rev(brewer.pal(n = 7, name ="RdPu")))(1)) + 
    facet_wrap(~ tissue, scales = 'free_x') + geom_tile() +
    geom_text(aes(label = pval))


p.6d_ <- ggarrange(
    p.6d + theme(legend.position = "none"), 
    ggarrange(get_legend(p.6d),
              bottom = text_grob("p-value\n*\t<= 0.05\n**\t<= 0.01\n***\t<= 0.001"),
              ncol = 1, nrow = 3),
    ncol = 2, widths = c(3,1)
)
```

## Figure 5d
```{r, warning=FALSE}
df <- readRDS("data/fig5d.rds")
p.5d <- ggplot(df, aes( x = dist_tss, y = fraction, colour = spec_celltype)) + geom_point(size = 1) +  facet_wrap(~ spec_celltype, ncol = 1) +
    theme_minimal() + scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x))) + labs(x = "Distance from TSS (bp)", y = "Fraction of cells") +
    theme( panel.grid.major = element_blank(), 
           panel.grid.minor = element_blank(),
           panel.background = element_blank(),
           legend.position="none",
           axis.text = element_text(size = 18),
           axis.text.x = element_text( size = 18 ),
           axis.title = element_text( size = 18) ,
           strip.text.x = element_text(size = 18)
           ) + scale_colour_manual(values = c(cbPalette, tritPalette, RColorBrewer::brewer.pal(8,colorcode))) +
   geom_text_repel(data=subset(df,dist_tss >= 5e5 | fraction >= .15), aes(dist_tss, fraction, label = key , colour = spec_celltype),color = "black", size = 5, box.padding = unit(2, "lines")
                    )

```


```{r echo=FALSE, fig.height=7, fig.retina=10, fig.width=7, message=FALSE, warning=FALSE}
p.6d_
```


```{r echo=FALSE, fig.height=8, fig.retina=10, fig.width=7, message=FALSE, warning=FALSE}
p.5d
```