# Case study – UpSet plot

Suppose you'd like to visualize some **common comorbidities** for asthma in FinnGen population. Perhaps the most intuitive method to see them is an **UpSet plot.**

There are two important parameters that shape the UpSet plot:

* `nsets`, the number of sets to look at (default `nsets = 5`)
* nintersects, the number of intersections to plot (default `nintersects = 40`)

If `nintersects` is set to `NA`, all intersections will be plotted.

```r
# function to get a character vector of FINNDENIDs for a group of endpoints

# function to get character vector of FINNGENID's for a list of endpoints
get_endpoint_ids <- function(...){
  endpoints <- list(...)
  sql<-paste0(
    "SELECT DISTINCT FINNGENID ",
    "FROM finngen-production-library.sandbox_tools_r10.endpoint_cohorts_r10_v1 ",
    "WHERE ENDPOINT IN (", paste0("'", endpoints, "'", collapse = ","), ")" 
  )
  tb <- bq_project_query(projectid, sql)
  df <- bq_table_download(tb) 
  pull(df, FINNGENID) 
}

asthma_cohort <- get_endpoint_ids('J10_ASTHMA', 'ASTHMA_MIXED')
chronic_rhinitis_cohort <- get_endpoint_ids('J10_CHRONRHINITIS')
sinusitis_cohort <- get_endpoint_ids('J10_SINUSITIS', 'J10_CHRONSINUSITIS', 'J10_UPPERINFEC')
reflux_cohort <- get_endpoint_ids('K11_REFLUX')
obesity_cohort <- get_endpoint_ids('ASTHMA_OBESITY')
sleep_apnea_cohort <- get_endpoint_ids('G6_SLEEPAPNO')

all <- unique(c(asthma_cohort, chronic_rhinitis_cohort, sinusitis_cohort, reflux_cohort, obesity_cohort, sleep_apnea_cohort))

asthma_cohort <- as.numeric(factor(asthma_cohort, levels = all))
chronic_rhinitis_cohort <- as.numeric(factor(chronic_rhinitis_cohort, levels = all))
sinusitis_cohort <- as.numeric(factor(sinusitis_cohort, levels = all))
reflux_cohort <- as.numeric(factor(reflux_cohort, levels = all))
obesity_cohort <- as.numeric(factor(obesity_cohort, levels = all))
sleep_apnea_cohort <- as.numeric(factor(sleep_apnea_cohort, levels = all))

inputList <- list(
  ASTHMA = asthma_cohort,
  RHINITIS = chronic_rhinitis_cohort,
  SINUSITIS = sinusitis_cohort,
  REFLUX = reflux_cohort,
  OBESITY = obesity_cohort,
  SLEEP_APNEA = sleep_apnea_cohort
)

UpSetR::upset(
  UpSetR::fromList(inputList),
  nsets = 6,
  nintersects = NA, 
  order.by = 'freq', 
  mb.ratio = c(0.7, .3), 
  text.scale = c(1.3, 1.3, 1.3, 0.8, 1.3, 1),
  set_size.show = TRUE, 
  set_size.angles = 0,
  number.angles = 35,
  set_size.scale_max = 240000
)

```

<figure><img src="/files/dacwZvaWL1B0sZmrlYMp" alt=""><figcaption></figcaption></figure>

**Location of the script's in the Sandbox**

Below is a path to the R Markdown file in Sandbox. This R Markdown file can be converted to an html page using "knit" command. The R Markdown is a plain text file, so you can copy code snippets that you need.

`/finngen/library-green/scripts/code_snippets/BigQuery_Templates_release.Rmd`


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