2abcdef.Rmd

---
title: "Figure 2"
output:
  html_document:
    df_print: paged
---


```{r message=FALSE, warning=FALSE}
suppressPackageStartupMessages(source("scripts/themes.R"))
tm.facs <- loadObject(filename = url("https://scfind.cog.sanger.ac.uk/indexes/tm_facs.rds"))
tm.10x <- loadObject(filename = url("https://scfind.cog.sanger.ac.uk/indexes/tm_10X.rds"))
```

## Table 2a
```{r paged.print=TRUE}
table.2a <- hyperQueryCellTypes(object = tm.facs, 
                    gene.list = c("Il2ra", "Ptprc", "Il7r", "Ctla4"))

table.2a[order(table.2a$pval, decreasing = F),]
```


## Figure 2b
```{r message=FALSE, warning=FALSE}
source("scripts/2b.R")

df.2b.p1 <- read.table("data/fig2b.csv", sep = ",", header = T, stringsAsFactors = F)
 
df.2b.p1$MarkerGenes <- factor(df.2b.p1$MarkerGenes, levels = c("CellMarker", "Seurat", "scfind"))

p1.vs.cellmarker <- ggplot(
  df.2b.p1, 
  aes( y = recall, x = precision, colour = MarkerGenes)
) + geom_density_2d(alpha = .6) + geom_point(alpha = .6) + main + 
scale_colour_manual("Marker Genes", values = tritPalette[c(2,4,3)], labels = c("CellMarker", "Seurat", "SCfind")) +
  ylab("Recall") + xlab("Precision") + xlim(0,1) + ylim(0,1) 
```

## Figure 2c
```{r message=FALSE, warning=FALSE}
df.2c.p2 <- read.table("data/fig2c.csv", sep = ",", header = T, stringsAsFactors = F)

p2.vs.cellmarker <- ggplot(
    df.2c.p2,
    aes(x = scfind,
        y = CellMarker,
        colour = Tissue)
    ) + geom_point(alpha = .5) + main + 
  xlab("SCfind") + ylab("CellMarker") + xlim(0,1) + ylim(0,1) + 
  guides(col = guide_legend(ncol = 2, title = "Tissue")) +
  geom_abline(inintercept = 0, colour = "red", linetype=2)
```

## Figure 2d
```{r message=FALSE, warning=FALSE}
df.2d <- read.table("data/fig2d.csv", sep = ",", header = T, stringsAsFactors = F)

p.2d <- ggplot(df.2d[!df.2d$no_of_genes %in% 5,]
               , aes(x = as.character(no_of_genes), y = score, fill = type)) + 
    main + 
    xlab("Number of genes") + ylab("Score") + 
    scale_fill_manual("Score type", values = cbPalette) + 
    geom_boxplot(size = .2, notch = T, outlier.size = .2) + 
    facet_grid(. ~ query)
```

## Figure 2e
```{r message=FALSE, warning=FALSE}
df.2e <- read.table("data/fig2e.csv", sep = ",", header = T, stringsAsFactors = F)

df.2e$atlas <- factor(df.2e$atlas, levels = legend_order)

p.2e <-  ggplot(df.2e, aes(x = values, fill = atlas)) + 
    geom_density(alpha=.8, aes(y = ..scaled..)) + 
        main  + theme(panel.margin = unit(-3, "lines"),strip.text.y = element_blank() ) +
    scale_y_continuous(breaks = c(1)) +
    labs(x = "Number of cell types", y = "Gene/peak\ndensity (arbitrary)", fill = "Atlas") + 
    scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x))) + 
    scale_fill_manual(values = RColorBrewer::brewer.pal(8,colorcode)) + 
    facet_grid(atlas~.)
```

## Figure 2f
```{r message=FALSE, warning=FALSE}
df.2f <- readRDS("data/fig2f.rds")

p.2f <- upset(fromList((df.2f)), 
              order.by="freq", 
              empty.intersections = "off", 
              sets.bar.color = RColorBrewer::brewer.pal(8,colorcode)[c(4:2,8)], 
              sets = c("TM, FACS","TM, 10X","MCA", "Eisenberg & Levanon" ), 
              mainbar.y.label = "House Keeping Gene\nIntersection", 
              text.scale = c(3), mb.ratio = c(.7,.3), number.angles = -45, scale.sets = "log10", point.size = 5, line.size = 3)
```

### Figure 2
```{r echo=FALSE, fig.height=5, fig.retina=10, fig.width=8, message=FALSE, warning=FALSE}
plot_grid(
  plot_grid(
    plot_grid(
      p1.vs.cellmarker + theme(legend.position = "none"),
      p2.vs.cellmarker + theme(legend.position = "none"),
      labels = c("B", "C")
    ),
    plot_grid(
      get_legend(p1.vs.cellmarker),
      get_legend(p2.vs.cellmarker), 
      nrow = 2, ncol = 1
    ),
    rel_widths = c(7,3)
  ),
  p.2d,
  ncol = 1, labels = c("", "D")
)

plot_grid(
    p.2e + theme(legend.position="right") + guides(fill = guide_legend(title.position = "top")),
    NULL,
    labels = c('E', 'F'),
    ncol = 2, nrow = 2,rel_heights = c(6,4)
)
```

```{r echo=FALSE, fig.height=9, fig.retina=20, fig.width=11, message=FALSE, warning=FALSE}
p.2f
```