---
title: "Slingshot"
author: "Nina-Lydia Kazakou"
date: "08/07/2021"
output: html_document
---

# Load libraries
```{r}
library(slingshot)
library(scales)
library(Seurat)
library(ggplot2)
library(RColorBrewer)
library(Seurat)
```

# Set the colour pallete 
```{r}
mypal <- pal_npg("nrc", alpha = 0.7)(10)
mypal2 <-pal_tron("legacy", alpha = 0.7)(7)
mypal3 <- pal_lancet("lanonc", alpha = 0.7)(9)
mypal4 <- pal_simpsons(palette = c("springfield"), alpha = 0.7)(16)
mypal5 <- pal_rickandmorty(palette = c("schwifty"), alpha = 0.7)(6)
mypal6 <- pal_futurama(palette = c("planetexpress"), alpha = 0.7)(5)
mypal7 <- pal_startrek(palette = c("uniform"), alpha = 0.7)(5)
mycoloursP<- c(mypal, mypal2, mypal3, mypal4, mypal5, mypal6, mypal7)
show_col(mycoloursP, labels =F)
```

# Load object
```{r}
alt.co.oligos <- readRDS(here("data", "Oligos_only", file = "alt.co.oligos.rds"))
head(alt.co.oligos.rds@meta.data)

Idents(alt.co.oligos.rds) <- "ClusterID"
DimPlot(alt.co.oligos.rds, cols = mycoloursP, pt.size = 1, label = TRUE) & NoAxes()
```

# Slingshot does not support ggplot2. Workaround:
```{r}
cell_pal <- function(cell_vars, pal_fun,...) {
  if (is.numeric(cell_vars)) {
    pal <- pal_fun(100, ...)
    return(pal[cut(cell_vars, breaks = 100)])
  } else {
    categories <- sort(unique(cell_vars))
    pal <- setNames(pal_fun(length(categories), ...), categories)
    return(pal[cell_vars])
  }
}
```

# Run Slingshot on the whole oligo_subset
```{r}
# For the whole dataset, I will set as starting point the primitive OPCs (cluster 0)
sds_alt.co.oligos <- slingshot(Embeddings(alt.co.oligos, "umap"), clusterLabels = alt.co.oligos$ClusterID, start.clus = 0, stretch = 0) 
cell_colors_clust <- cell_pal(alt.co.oligos$ClusterID, hue_pal())
plot(reducedDim(sds_alt.co.oligos), col = cell_colors_clust, pch = 16, cex = 0.5) 
lines(sds_alt.co.oligos, lwd = 2, type = 'lineages', col = 'black')
```

# Create a slingshot trajectory for each timepoint seperately
```{r}
# Week 16
Idents(alt.co.oligos) <- "Sample"
week_16 <- subset(alt.co.oligos, ident = "wk16")

sds_week_16 <- slingshot(Embeddings(week_16, "umap"), clusterLabels = week_16$ClusterID, start.clus = 0, stretch = 0) 
cell_colors_clust <- cell_pal(week_16$ClusterID, hue_pal())
plot(reducedDim(sds_week_16), col = cell_colors_clust, pch = 16, cex = 0.5) 
lines(sds_week_16, lwd = 2, type = 'lineages', col = 'black')
``` 

```{r}
# Week 21
Idents(alt.co.oligos) <- "Sample"
week_21 <- subset(alt.co.oligos, ident = "wk21")

sds_week_21 <- slingshot(Embeddings(week_21, "umap"), clusterLabels = week_21$ClusterID, start.clus = 0, stretch = 0) 
cell_colors_clust <- cell_pal(week_21$ClusterID, hue_pal())
plot(reducedDim(sds_week_21), col = cell_colors_clust, pch = 16, cex = 0.5) 
lines(sds_week_21, lwd = 2, type = 'lineages', col = 'black')
``` 

```{r}
# Week 25
Idents(alt.co.oligos) <- "Sample"
week_25 <- subset(alt.co.oligos, ident = "wk25")

sds_week_25 <- slingshot(Embeddings(week_25, "umap"), clusterLabels = week_25$ClusterID, start.clus = 0, stretch = 0) 
cell_colors_clust <- cell_pal(week_25$ClusterID, hue_pal())
plot(reducedDim(sds_week_25), col = cell_colors_clust, pch = 16, cex = 0.5) 
lines(sds_week_25, lwd = 2, type = 'lineages', col = 'black')
```