17-exprs-overview-reads.Rmd

---
output: html_document
---

## Data visualization (Reads)

```{r, message=FALSE, warning=FALSE}
library(scater)
options(stringsAsFactors = FALSE)
reads <- readRDS("tung/reads.rds")
reads.qc <- reads[rowData(reads)$use, colData(reads)$use]
endog_genes <- !rowData(reads.qc)$is_feature_control
```

```{r, echo=FALSE}
library(knitr)
opts_chunk$set(out.width='90%', fig.align = 'center')
```

```{r expr-overview-pca-before-qc-reads1, fig.cap = "PCA plot of the tung data"}
plotPCA(
    reads[endog_genes, ],
    exprs_values = "counts",
    colour_by = "batch",
    size_by = "total_features",
    shape_by = "individual"
)
```

```{r expr-overview-pca-before-qc-reads2, fig.cap = "PCA plot of the tung data"}
plotPCA(
    reads[endog_genes, ],
    exprs_values = "logcounts_raw",
    colour_by = "batch",
    size_by = "total_features",
    shape_by = "individual"
)
```

```{r expr-overview-pca-after-qc-reads, fig.cap = "PCA plot of the tung data"}
plotPCA(
    reads.qc[endog_genes, ],
    exprs_values = "logcounts_raw",
    colour_by = "batch",
    size_by = "total_features",
    shape_by = "individual"
)
```

```{r expr-overview-tsne-before-qc-reads, fig.cap = "tSNE map of the tung data"}
plotTSNE(
    reads[endog_genes, ],
    exprs_values = "logcounts_raw",
    perplexity = 130,
    colour_by = "batch",
    size_by = "total_features",
    shape_by = "individual",
    rand_seed = 123456
)
```

```{r expr-overview-tsne-after-qc-reads, fig.cap = "tSNE map of the tung data"}
plotTSNE(
    reads.qc[endog_genes, ],
    exprs_values = "logcounts_raw",
    perplexity = 130,
    colour_by = "batch",
    size_by = "total_features",
    shape_by = "individual",
    rand_seed = 123456
)
```

```{r expr-overview-tsne-after-qc-exercise2-1, fig.cap = "tSNE map of the tung data (perplexity = 10)", echo=FALSE}
plotTSNE(
    reads.qc[endog_genes, ],
    exprs_values = "logcounts_raw",
    perplexity = 10,
    colour_by = "batch",
    size_by = "total_features",
    shape_by = "individual",
    rand_seed = 123456
)
```

```{r expr-overview-tsne-after-qc-exercise2-2, fig.cap = "tSNE map of the tung data (perplexity = 200)", echo=FALSE}
plotTSNE(
    reads.qc[endog_genes, ],
    exprs_values = "logcounts_raw",
    perplexity = 200,
    colour_by = "batch",
    size_by = "total_features",
    shape_by = "individual",
    rand_seed = 123456
)
```

```{r}
sessionInfo()
```