115_wgs_impact_cbioportal.Rmd

---
title: "cBioPortal"
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: "115_wgs_impact_cbioportal.Rmd"
---

# cBioPortal

```{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(gdata)
library(stringr)
library(data.table)
library(openxlsx)
library(gtable)
library(cowplot)
```

## Database

```{r}

source("src/global_vars.R")

db_all <- db
db_filtered <- db

```

### Filtering

```{r}

# Separate bulk normal and bulk tumor WGS samples
db_filtered$sequencing_bulk_dna <- db_filtered$sequencing_bulk_dna %>%
  filter(tme_inclusion_status == "Yes")

db_filtered$sequencing_bulk_dna_tumor <- db_filtered$sequencing_bulk_dna %>%
  filter(!is.na(tumor_site))

db_filtered$sequencing_bulk_dna_normal <- db_filtered$sequencing_bulk_dna %>%
  filter(is.na(tumor_site))

# Separate bulk normal and bulk tumor IMPACT samples
db_filtered$sequencing_msk_impact_custom <- db_filtered$sequencing_msk_impact_custom %>%
  filter(tme_inclusion_status == "Yes")

db_filtered$sequencing_msk_impact_custom_tumor <- db_filtered$sequencing_msk_impact_custom %>%
  filter(!is.na(tumor_site))

db_filtered$sequencing_msk_impact_custom_normal <- db_filtered$sequencing_msk_impact_custom %>%
  filter(is.na(tumor_site))

# Separate bulk normal and bulk tumor IMPACT samples
db_filtered$he_slide <- db_filtered$he_slide %>%
  filter(tme_inclusion_status == "Yes")

```

## Patient metadata

```{r}

url <- "tables/patient_metadata_edits.xlsx"
data_clinical_patient <- read.xlsx(url)

# url <- "/work/shah/vazquezi/projects/datahub_shahlab/msk_spectrum/data_clinical_patient.txt"
# data_clinical_patient <- read_tsv(url, skip = 4)

data_clinical_patient <- data_clinical_patient %>%
  rename(
    "PATIENT_ID" = "patient_dmp_id",
    "PATIENT_DISPLAY_NAME" = "patient_id"
    ) %>%
  rename_with(toupper) %>%
  relocate(PATIENT_ID, PATIENT_DISPLAY_NAME)

data_clinical_patient

```

```{r}

write_tsv(data_clinical_patient, "tables/115_wgs_impact_cbioportal/data_clinical_patient.txt", na = "")

```

## Sample metadata

### WGS

```{r}

data_clinical_sample_wgs <- db_filtered$sequencing_bulk_dna_tumor %>%
  left_join(
    db$patients %>%
      select(patient_id, patient_dmp_id),
    by = "patient_id"
  ) %>%
  select(
    "SAMPLE_ID" = "isabl_experiment_system_id",
    "PATIENT_ID" = "patient_dmp_id",
    "SAMPLE_TYPE" = "tumor_type",
    "PATIENT_DISPLAY_NAME" = "patient_id",
    "TUMOR_MEGASITE" = "tumor_megasite",
    "TUMOR_SUPERSITE" = "tumor_supersite",
    "TUMOR_SITE" = "tumor_site",
    "TUMOR_SUBSITE" = "tumor_subsite",
    "THERAPY"="therapy",
    "PROCEDURE"="procedure",
    "PROCEDURE_TYPE"="procedure_type"
  ) %>%
  mutate(
    INSTITUTE = "MSKCC",
    SOMATIC_STATUS = "Matched",
    SAMPLE_CLASS = "Tumor",
    GENE_PANEL = "WGS"
  ) %>%
  mutate(
    METASTATIC_SITE = ifelse(SAMPLE_TYPE == "Metastasis", TUMOR_SUBSITE, "Not Applicable"),
    PRIMARY_SITE = ifelse(SAMPLE_TYPE == "Primary", TUMOR_SUBSITE, "Adnexa")
  )

data_clinical_sample_wgs

```

### IMPACT

```{r}

url <- "/work/shah/vazquezi/projects/datahub_shahlab/msk_spectrum/data_clinical_sample.txt"
data_clinical_sample_impact <- read_tsv(url, skip = 4)
data_clinical_sample_impact_header <- read_tsv(url, n_max = 4)

data_clinical_sample_impact <- data_clinical_sample_impact %>%
  filter(SAMPLE_ID %in% db_filtered$sequencing_msk_impact_custom_tumor$impact_dmp_sample_id) %>%
  select(
    -c("DATE_ADDED","MONTH_ADDED","WEEK_ADDED","CRDB_SURVEY_COMMENTS","MGMT_STATUS","WHO_GRADE","MSK_SLIDE_ID","SAMPLE_TYPE"),
    -contains("CVR_TMB")
    ) %>%
  left_join(
    db_filtered$sequencing_msk_impact_custom %>%
      select(
        "impact_dmp_sample_id",
        "PATIENT_DISPLAY_NAME"="patient_id",
        "TUMOR_MEGASITE"="tumor_megasite",
        "TUMOR_SUPERSITE"="tumor_supersite",
        "TUMOR_SITE"="tumor_site",
        "TUMOR_SUBSITE"="tumor_subsite",
        "SAMPLE_TYPE"="tumor_type",
        "THERAPY"="therapy",
        "PROCEDURE"="procedure",
        "PROCEDURE_TYPE"="procedure_type"
      ),
    by = c("SAMPLE_ID"="impact_dmp_sample_id")
  ) %>%
  mutate(
    METASTATIC_SITE = ifelse(SAMPLE_TYPE == "Metastasis", TUMOR_SUBSITE, "Not Applicable"),
    PRIMARY_SITE = ifelse(SAMPLE_TYPE == "Primary", TUMOR_SUBSITE, "Adnexa")
  )

data_clinical_sample_impact

```

### Merged

```{r}

data_clinical_sample <- bind_rows(
  data_clinical_sample_impact,
  data_clinical_sample_wgs
) %>%
  # Sort by WGS/IMPACT and patient
  arrange(desc(GENE_PANEL),PATIENT_ID) %>%
  # # Fill missing WGS metadata using IMPACT metadata
  # group_by(PATIENT_DISPLAY_NAME) %>% 
  # fill(CANCER_TYPE, CANCER_TYPE_DETAILED, ONCOTREE_CODE, .direction = "updown") %>%
  # ungroup %>%
  # Homogenise WGS/IMPACT metadata for diagnosis
  mutate(
    CANCER_TYPE = "Ovarian Cancer",
    CANCER_TYPE_DETAILED = "High-Grade Serous Ovarian Cancer",
    ONCOTREE_CODE = "HGSOC"
  ) %>%
  # Add metadata about site-matched H&E images
  left_join(
    db_filtered$he_slide %>%
      select(
        "MSK_SLIDE_ID"="image_id",
        "PATIENT_DISPLAY_NAME"="patient_id",
        "TUMOR_SITE"="tumor_site",
        "PROCEDURE"="procedure"
        ),
    by = c("PATIENT_DISPLAY_NAME","TUMOR_SITE","PROCEDURE")
  ) %>%
  mutate(
    PATH_SLIDE_EXISTS = ifelse(!is.na(MSK_SLIDE_ID), "YES", "NO")
  ) %>%
  relocate(MSK_SLIDE_ID, .after = PATH_SLIDE_EXISTS)

data_clinical_sample

```

```{r}

write_tsv(data_clinical_sample, "tables/115_wgs_impact_cbioportal/data_clinical_sample.txt", na = "")

```

## Mutational signatures

```{r}

url <- "tables/mutational_signatures.xlsx"
data_clinical_supp <- read.xlsx(url)

data_clinical_supp <- data_clinical_supp %>%
  rename(
    "PATIENT_DISPLAY_NAME" = "patient_id"
  ) %>%
  rename_with(toupper) %>%
  left_join(
    db$patients %>%
      select(
        "PATIENT_ID" = "patient_dmp_id",
        "PATIENT_DISPLAY_NAME" = "patient_id"
      ),
    by = "PATIENT_DISPLAY_NAME"
  ) %>%
  # filter(PATIENT_DISPLAY_NAME %in% tme_patients) %>%
  relocate(PATIENT_ID, PATIENT_DISPLAY_NAME)

data_clinical_supp

```

```{r}

write_tsv(data_clinical_supp, "tables/115_wgs_impact_cbioportal/data_clinical_supp.txt", na = "")

```