---
title: "Transcriptomics visualization"
author: "mhoque"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    vertical_layout: scroll
    social: menu
    theme: cerulean
    css: style.css
    source_code: embed
---

```{r setup, include=FALSE}
library(flexdashboard)
library(knitr)
load(file="transcriptomics_viz.RData")

```

Row  
-----------------------------------------------------------------------

### Volcano Plot

```{r}
volcano_plot

```

>Volcano plot showing up- and down-regulated genes.

### PCA Plot

```{r}
pca_plot

```

>PCA plot: control vs treatment

Row
-----------------------------------------------------------------------

### Heatmap 

```{r}

heatmap

```

>Heatmap of highly significant genes (lfc > 2 and p-value < 10e-10)


### Pathview

```{r}
include_graphics("pae03070.pae.kegg.png", dpi=600)

```

> Example pathway enrichment plot

Row {data-width=1000}
-------------------------------------

### Table 

```{r}
fc_table_sig

```

>Details of the differentially expressed genes (1 < lfc < -1 and p < 0.05).