---
title: "RA 3D"
author: "Ludvig Larsson"
date: "1/3/2020"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r load_libs}
library(STutility)
#saveRDS(se, file = "~/10x/R_objects/se_RA")
se <- readRDS("~/10x/R_objects/se_RA")
```


## Create spotfiles

```{r seurat}

spotfiles <- list.files("~/RA_project/data/Patient2/HE_spots_xy_files", full.names = T)
xys <- lapply(spotfiles, function(f) {
  df <- read.table(file = f, header = T, sep = "\t", stringsAsFactors = F)
  xy <- data.frame(do.call(rbind, strsplit(rownames(df), split = "_")), stringsAsFactors = F)
  df <- setNames(cbind(xy, xy, df), nm = c("x", "y", "new_x", "new_y", "pixel_x", "pixel_y"))
  df <- as.data.frame(lapply(df, as.numeric))
})

dir.create(path = "~/RA_project/data/Patient2/spotfiles")
for (i in seq_along(xys)) {
  write.table(x = xys[i], file = paste0("~/RA_project/data/Patient2/spotfiles/selection_", i, ".tsv"), sep = "\t", row.names = F, col.names = T, quote = F)
}

```

Create gene_id conversion data.frame

```{r}

ensids <- read.table("~/Fetal_heart_project/annotation/genes.tsv", header = T, stringsAsFactors = F)
ensids$gene_id <- substr(x = ensids$gene_id, start = 1, stop = 15)
ensids <- ensids[-which(duplicated(ensids$gene_id)), ]
write.table(x = ensids, file = "~/RA_project/genes.tsv", quote = F, sep = "\t", row.names = F, col.names = T)

```

## Load data

```{r}

samples <- list.files("~/RA_project/data/tsv", full.names = T)[5:11]
imgs <- list.files(pattern = ".jpg", "~/RA_project/data/Patient2/images", full.names = T)[1:7]
spotfiles <- list.files("~/RA_project/data/Patient2/spotfiles", full.names = T)

infoTable <- data.frame(samples, imgs, spotfiles, stringsAsFactors = FALSE)

```

## Read input

```{r seurat}

se <- InputFromTable(infoTable, 
                     platform = "1k", 
                     annotation = ensids, 
                     min.gene.count = 300, 
                     min.spot.count = 1e3)

```

## Load images

```{r load_imgs}

se <- LoadImages(se, time.resolve = F)

```

## Align images

```{r manual_align}

se <- MaskImages(se)
se <- ManualAlignImages(se, reference.index = 4)

```

## Check alignment

```{r plot_aligned}

ImagePlot(se, method = "raster")

```

## Normalize data

```{r normalization, warning=F, message=F}

se@meta.data$sample_id <- paste0("sample_", se@tools$Staffli@meta.data$sample)

se <- SCTransform(se, vars.to.regress = c("sample_id"))

```

## Create 3D stack

```{r 3D_stack}

se <- Create3DStack(se)

```

## Find spatial features

```{r spatcor}

spatgenes <- CorSpatialGenes(se)
head(spatgenes, 20)

```

## Plotting in 3D

```{r 3D_plot}

FeaturePlot3D(se, features = "SELL", pt.size = 0.5, cols = c("lightgray", "lightgray", "mistyrose", "red", "dark red", "black"))

```

## Run NMF

```{r nmf}

se <- RunNMF(se, nfactors = 10, n.cores = 7)

```
<br>
## Plot factors
CCL21 - Inhibits hemopoiesis and stimulates chemotaxis. Chemotactic in vitro for thymocytes and activated T-cells, but not for B-cells, macrophages, or neutrophils. 
CCL19 -  Recombinant CCL19 shows potent chemotactic activity for T-cells and B-cells but not for granulocytes and monocytes.
EVL - Ena/VASP proteins are actin-associated proteins involved in a range of processes dependent on cytoskeleton remodeling and cell polarity such as axon guidance and lamellipodial and filopodial dynamics in migrating cells.
CD3E + SELL CD4 T-cell markers.
<br>
```{r nmf1_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 1, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 1, dark.theme = T),
  ncol = 2)

```
<br>
I think this factor must be some artefact along the edges. Maybe the cells have initiated a stress response or something ...
<br>
```{r nmf2_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 2, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 2, dark.theme = T),
  ncol = 2)

```
<br>
MZB1 = B/plasma cell marker 
<br>
```{r nmf3_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 3, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 3, dark.theme = T),
  ncol = 2)

```
<br>
MZB1 B cell marker, HBA1/HBA2 blood markers
<br>
```{r nmf4_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 4, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 4, dark.theme = T),
  ncol = 2)

```
<br>
CD79A/CD79B - B lymphocyte antigen receptor
CD52 - Present on mature lymphocytes
<br>
```{r nmf5_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 5, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 5, dark.theme = T),
  ncol = 2)

```
<br>
Ribosomal protein genes ...
<br>
```{r nmf6_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 6, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 6, dark.theme = T),
  ncol = 2)

```
<br> 
C1QB/C1QC - Antigen presenting cells, e.g. Denritic cells macrophages?
CFD - This protease catalyzes the cleavage of factor B, the rate-limiting step of the alternative pathway of complement activation.
CD14 - (cluster of differentiation 14) is a human protein made mostly by macrophages as part of the innate immune system
<br>
```{r nmf7_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 7, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 7, dark.theme = T),
  ncol = 2)

```
<br>
CD6 on surface of T-cells
SIGIRR - Acts as a negative regulator of the Toll-like and IL-1R receptor signaling pathways
<br>
```{r nmf8_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 8, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 8, dark.theme = T),
  ncol = 2)

```
<br>
HLA-DRA/HLA-DBQ1 - Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages)
TMSB4X - This gene encodes an actin sequestering protein which plays a role in regulation of actin polymerization. The protein is also involved in cell proliferation, migration, and differentiation.
VIM - This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells.
MS4A1 - B cell marker
<br>
```{r nmf9_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 9, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 9, dark.theme = T),
  ncol = 2)

```
<br>
HLA-DRB1 - Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages).
CD14 - (cluster of differentiation 14) is a human protein made mostly by macrophages as part of the innate immune system

<br>
```{r nmf10_plot, fig.width=8, fig.height=8}

cowplot::plot_grid(
  ST.DimPlot(se, reduction = "NMF", dims = 10, 
             pt.size = 1.5, dark.theme = T, ncol = 2,
             cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"), 
             center.zero = F),
  FactorGeneLoadingPlot(se, factor = 10, dark.theme = T),
  ncol = 2)

```

### HSVPlot

```{r hsv2d, fig.width=10, fig.height=6}

p1 <- HSVPlot(se, features = paste0("factor_", c(1, 10, 5, 7)), pt.size = 1.5)
c(df1, df2) %<-% SummarizeAssocFeatures(se, dims = c(1, 10, 5, 7))

p2 <- swne::ggHeat(df2[nrow(df2):1, ], rescaling = "column") +
  scale_fill_gradientn(colours = viridis::magma(n = 11)) +
  DarkTheme() +
  theme(plot.background = element_rect(fill = "black", colour = "black"), plot.margin = margin(2, 2, 2, 2, "cm"))

cowplot::plot_grid(p1, p2, ncol = 2)

```

### Plot 3D

```{r NMF_3D}

DimPlot3D(se, reduction = "NMF", dims = 7, dark.theme = T, cols = c("black", "navyblue", "cyan", "yellow", "red", "dark red"))

```

### HSVPlot 3D

```{r HSV_NMF_3D}

HSVPlot3D(se, features = paste0("factor_", c(1, 10, 5, 7)), dark.theme = T)
htmlwidgets::saveWidget(HSVPlot3D(se, features = paste0("factor_", c(1, 10, 5, 7)), dark.theme = T), "~/STUtility_backup/figures/RA_3D.html")

```

## Date

```{r date}
date()
```

## Session Info

```{r sessioninfo}
sessionInfo()
```