---
title: Plotting Alignments
output:
  BiocStyle::html_document
---

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<!--
%% \VignetteEngine{knitr::rmarkdown}
%% \VignetteIndexEntry{Plotting Alignments}
-->

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
```

```{r, echo = FALSE}
apiKey <- Sys.getenv("GOOGLE_API_KEY")
if (nchar(apiKey) == 0) {
  warning(paste("To build this vignette, please setup the environment variable",
                "GOOGLE_API_KEY with the public API key from your Google",
                "Developer Console before loading the GoogleGenomics package,",
                "or run GoogleGenomics::authenticate."))
  knitr::knit_exit()
}
```

# Plotting Alignments

Let's take a look at the reads that overlap [rs9536314](http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=9536314) for sample NA12893 within the [Illumina Platinum Genomes](https://cloud.google.com/genomics/data/platinum-genomes) dataset.  This SNP resides on chromosome 13 at position 33628137 in 0-based coordinates.
```{r}
# Authenticated on package load from the env variable GOOGLE_API_KEY.
suppressPackageStartupMessages(library(GoogleGenomics))

reads <- getReads(readGroupSetId="CMvnhpKTFhDyy__v0qfPpkw",
                  chromosome="chr13",
                  start=33628130,
                  end=33628145)
alignments <- readsToGAlignments(reads)
```

Display the basic alignments and coverage data:
```{r coverage}
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(ggbio))
alignmentPlot <- autoplot(alignments, aes(color=strand, fill=strand))
coveragePlot <- ggplot(as(alignments, "GRanges")) +
                stat_coverage(color="gray40", fill="skyblue")
tracks(alignmentPlot, coveragePlot,
       xlab="Reads overlapping rs9536314 for NA12893")
```

You could also display the spot on the chromosome these alignments came from:
```{r ideogram}
ideogramPlot <- plotIdeogram(genome="hg19", subchr="chr13")
ideogramPlot + xlim(as(alignments, "GRanges"))
```

### Provenance
Package versions used:
```{r}
sessionInfo()
```