112_scrna_cellxgene.Rmd

---
title: "scRNA data conversion for cellxgene"
subtitle: "MSK SPECTRUM"
author:
  - "Ignacio Vazquez-Garcia"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: 
  html_document:
    highlight: tango
    df_print: paged
    code_folding: hide
    fig_align: center
    toc: true
    toc_float: true
    toc_depth: 3
    number_sections: yes
params:
   rmd: "112_scrna_cellxgene.Rmd"
---

```{r setup, include=FALSE}
# Global knit options
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())

# Global chunk options
knitr::opts_chunk$set(echo=FALSE, tidy=TRUE, warning=FALSE, message=FALSE)
```

```{r}

library(tidyverse)
library(Seurat)
library(SeuratData)
library(SeuratDisk)
library(sceasy)
library(googlesheets4)
library(cowplot)

library(reticulate)
use_condaenv('cellxgene')

source("src/global_vars.R")
source("src/metadata.R")

```

## Load data

```{r}

seu_obj <- readr::read_rds("/work/shah/users/uhlitzf/data/SPECTRUM/freeze/v7/outs_pre/integrated_seurat.rds")

```

## Load metadata

```{r}

gids <- list(
  "organism_ontology"="910670315",
  "tissue_ontology"="1819990913",
  "assay_ontology"="150407398",
  "suspension_ontology"="533715780",
  "disease_ontology"="1550965376",
  "cell_type_super_ontology"="2137427075",
  "cell_type_sub_ontology"="120791258",
  "ethnicity_ontology"="1904472753",
  "development_stage_ontology"="722315336",
  "sex_ontology"="1100516779"
)

url_template <- "https://docs.google.com/spreadsheets/d/15RWlyM8EfB7CgFGc22nIw0yBErkdHz0EFf0DYBMae2M/export?format=tsv&id=15RWlyM8EfB7CgFGc22nIw0yBErkdHz0EFf0DYBMae2M&gid="

ontology_list <- gids %>% 
  imap(~ str_c(url_template,.x)) %>%
  map(~read_tsv(.))

```

## Map cellxgene metadata

```{r}

source("src/metadata.R")

# Duplicate Seurat object to add annotations
seu_obj_annotated <- seu_obj
scrna_meta_cell_tbl <- seu_obj_annotated@meta.data

# Add patient metadata
scrna_meta_cell_tbl <- add_cellxgene_patient_metadata(scrna_meta_cell_tbl, db, ontology_list)

# Add sample metadata
scrna_meta_cell_tbl <- add_cellxgene_sample_metadata(scrna_meta_cell_tbl, db, ontology_list)

# Add cell metadata
scrna_meta_cell_tbl <- add_cellxgene_cell_metadata(scrna_meta_cell_tbl, db, ontology_list)

# 
# # Add columns with constant values for all samples based on ontology table
# 
# ## Organism ontology
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # organism & organism_ontology_term_id (Example: Homo sapiens, NCBITaxon:9606)
#   add_column(
#     ontology_list$organism_ontology %>%
#       select(c("organism", "organism_ontology_term_id")),
#   ) %>%
#   select(-c("organism"))
# 
# # Add columns with sample-dependent values by mapping to ontology table
# 
# ## Cell type ontology
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # Remap monocytes to myeloid cells to follow convention used in paper
#   mutate(cell_type = ifelse(cell_type == "Monocyte", "Myeloid.cell", cell_type)) %>% 
#   # cell_type & cell_type_ontology_term_id (Epithelial Cell, CL:0000066)
#   left_join(
#     ontology_list$cell_type_super_ontology %>%
#       select(c("cell_type", "cell_type_ontology_term_id")),
#     by = "cell_type"
#   ) %>%
#   rename(c("author_cell_type" = "cell_type")) %>%
#   select(-c("cell_type_super","seurat_clusters"))
# 
# # Tissue ontology
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # Add sample assay
#   left_join(
#     db$sequencing_scrna %>%
#       select(c("isabl_id","tumor_subsite")),
#     by = c("sample"="isabl_id")
#   ) %>%
#   # tissue & tissue_ontology_term_id
#   left_join(
#     ontology_list$tissue_ontology %>%
#       select(c("tumor_subsite", "tissue", "tissue_ontology_term_id")),
#     by = "tumor_subsite"
#   ) %>%
#   select(-c("tumor_subsite","tissue"))
# 
# ## Assay ontology
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # Add sample assay
#   left_join(
#     db$sequencing_scrna %>%
#       select(c("isabl_id","platform")),
#     by = c("sample"="isabl_id")
#   ) %>%
#   # assay & assay_ontology_term_id (Example: 10xV2 assay, EFO:0009899)
#   left_join(
#     ontology_list$assay_ontology %>%
#       select(c("platform", "assay", "assay_ontology_term_id")),
#     by = "platform"
#   ) %>%
#   select(-c("platform","assay"))
# 
# ## Suspension type ontology
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # Add suspension_type
#   mutate(
#     suspension_type = "cell"
#   )
# 
# ## Disease ontology
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # Add sample assay
#   left_join(
#     db$gyn_diagnosis %>%
#       select(c("patient_id","gyn_diagnosis_histology")),
#     by = "patient_id"
#   ) %>%
#   # disease & disease_ontology_term_id (MONDO or normal/PATO:0000461 if healthy)
#   left_join(
#     ontology_list$disease_ontology %>%
#       select(c("gyn_diagnosis_histology", "disease", "disease_ontology_term_id")),
#     by = "gyn_diagnosis_histology"
#   ) %>%
#   select(-c("gyn_diagnosis_histology","disease"))
# 
# ## Ethnicity ontology
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # Add patient ethnicity
#   left_join(
#     db$patients %>%
#       select(c("patient_id","patient_race")), 
#     by = "patient_id"
#   ) %>%
#   # ethnicity & ethnicity_ontology_term_id (Example: Asian, HANCESTRO:0008, ‘unknown’ if info unavailable)
#   left_join(
#     ontology_list$ethnicity_ontology %>%
#       select(c("patient_race", "ethnicity", "ethnicity_ontology_term_id")),
#     by = "patient_race"
#   ) %>%
#   select(-c("patient_race","ethnicity"))
# 
# ## Age ontology
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # Add patient age
#   left_join(
#     db$patients %>%
#       select(c("patient_id","patient_age")), 
#     by = "patient_id"
#   ) %>%
#   # development_stage & development_stage_ontology_term_id field (20-year-old human stage,HsapDv:0000114, ‘unknown’ if info unavailable)
#   left_join(
#     ontology_list$development_stage_ontology %>%
#       select(c("patient_age", "development_stage", "development_stage_ontology_term_id")),
#     by = "patient_age"
#   ) %>%
#   select(-c("patient_age","development_stage"))
# 
# ## Sex ontology
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # Add patient sex
#   left_join(
#     db$patients %>%
#       select(c("patient_id","patient_gender")), 
#     by = "patient_id"
#   ) %>%
#   # sex & sex_ontology_term_id field – male (PATO:0000384) or female (PATO:0000383) ('unknown' if info unavailable)
#   left_join(
#     ontology_list$sex_ontology %>%
#       select(c("patient_gender", "sex", "sex_ontology_term_id")),
#     by = "patient_gender"
#   ) %>%
#   select(-c("patient_gender","sex"))
# 
# ## Donor identifier
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   # Add patient identifier
#   mutate(
#     donor_id = patient_id
#   ) %>%
#   select(-c("patient_id","batch"))
# 
# ## Sample identifier
# scrna_meta_cell_tbl <- scrna_meta_cell_tbl %>%
#   rename(
#     c("author_sample_id" = "sample")
#   ) %>%
#   # Add sample assay
#   left_join(
#     db$sequencing_scrna %>%
#       select(c("isabl_id","tumor_supersite","tumor_site","tumor_subsite","sort_parameters","therapy","procedure","procedure_type")) %>% 
#       rename(
#         c("sample_id" = "isabl_id")
#       ) %>%
#       rename_with( ~ paste("author", .x, sep = "_")),
#     by = "author_sample_id"
#   )

scrna_meta_cell_tbl

seu_obj_annotated@meta.data <- scrna_meta_cell_tbl

```

## Export data

### Metadata

```{r}

write_tsv(scrna_meta_cell_tbl, "release/cellxgene/scrna_cell_metadata.tsv")

```

### Seurat

```{r}

seu_obj_annotated_lite <- 
  Seurat::DietSeurat(
    seu_obj_annotated,
    counts = TRUE,
    data = TRUE,
    scale.data = FALSE,
    assays = "RNA",
    dimreducs = c("pca","umap50")
)

```

```{r}

# Save Seurat object as h5Seurat
SeuratDisk::SaveH5Seurat(
  seu_obj_annotated, 
  filename = "release/cellxgene/seu_obj_annotated_seuratdisk.h5Seurat",
  overwrite = TRUE,
  verbose = TRUE
)

# Convert h5Seurat file to h5ad file
SeuratDisk::Convert(
  "release/cellxgene/seu_obj_annotated_seuratdisk.h5Seurat", 
  dest = "h5ad",
  assay = "RNA",
  overwrite = TRUE,
  verbose = TRUE
)

```

```{r}

# Save Seurat object as h5Seurat
SeuratDisk::SaveH5Seurat(
  seu_obj_annotated_lite, 
  filename = "release/cellxgene/seu_obj_annotated_lite_seuratdisk.h5Seurat",
  overwrite = TRUE,
  verbose = TRUE
)

# Convert h5Seurat file to h5ad file
SeuratDisk::Convert(
  "release/cellxgene/seu_obj_annotated_lite_seuratdisk.h5Seurat", 
  dest = "h5ad",
  assay = "RNA",
  overwrite = TRUE,
  verbose = TRUE
)

```

### sceasy

```{r}

# sceasy::convertFormat(
#   seu_obj_annotated_lite, 
#   assay='RNA', 
#   from="seurat", 
#   to="anndata", 
#   main_layer='data', 
#   transfer_layers='counts', 
#   drop_single_values=FALSE, 
#   outFile='seu_obj_annotated_lite_scgene.h5ad'
# )

```