literate-programming-demo.R

## ----one time setup, eval=FALSE------------------------------------------
## ### To install the bigrquery package.  The currently released version 0.3.0 does not yet
## ### have the parameter to use Standard SQL instead of Legacy SQL, so we install from github.
## library(devtools)
## install_github('rstats-db/bigrquery')

## ----initialize, message=FALSE, warning=FALSE----------------------------
library(bigrquery)
library(ggplot2)
library(xtable)

## ----eval=FALSE----------------------------------------------------------
## ######################[ CHANGE ME ]##################################
## # This codelab assumes that the current working directory is where the Rmd file resides.
## setwd("/YOUR/PATH/TO/getting-started-bigquery/RMarkdown")
## 
## # Set the Google Cloud Platform project id under which these queries will run.
## project <- "YOUR-PROJECT-ID"
## #####################################################################

## ------------------------------------------------------------------------
# By default this codelab runs upon the Illumina Platinum Genomes Variants.
# Change the table here if you wish to run these queries against a different table.
theTable <- "genomics-public-data.platinum_genomes.variants"

## ------------------------------------------------------------------------
DisplayAndDispatchQuery <- function(queryUri) {
  # Read in the SQL from a file or URL.
  querySql <- readChar(queryUri, nchars=1e6)
  # Find and replace the table name placeholder with our table name.
  querySql <- sub("@THE_TABLE", theTable, querySql, fixed=TRUE)
  # Display the updated SQL.
  cat(querySql)
  # Dispatch the query to BigQuery for execution.
  query_exec(querySql, project, use_legacy_sql = FALSE)
}

## ----comment=NA----------------------------------------------------------
result <- DisplayAndDispatchQuery("../sql/sample-variant-counts-for-brca1.sql")

## ----result, comment=NA--------------------------------------------------
head(result)
summary(result)
str(result)

## ----viz, fig.align="center", fig.width=10-------------------------------
ggplot(result, aes(x=call_set_name, y=variant_count)) +
  geom_bar(stat="identity") + coord_flip() +
  ggtitle("Count of Variants Per Sample")

## ----comment=NA----------------------------------------------------------
result <- DisplayAndDispatchQuery("../sql/variant-level-data-for-brca1.sql")

## ----echo=FALSE, message=FALSE, warning=FALSE, comment=NA, results="asis"----
print(xtable(head(result)), type="html", include.rownames=F)

## ----comment=NA----------------------------------------------------------
result <- DisplayAndDispatchQuery("../sql/sample-level-data-for-brca1.sql")

## ----echo=FALSE, message=FALSE, warning=FALSE, comment=NA, results="asis"----
print(xtable(head(result)), type="html", include.rownames=F)

## ----provenance, comment=NA----------------------------------------------
sessionInfo()