extraplot.Rmd

# Plots from other packages

We will see two additional types of plots:

* Heat map (from package pheatmap)
* Venn diagram (from package VennDiagram)

## pheatmap function from the pheatmap package

A heatmap is a graphical representation of data where the values are represented with **colors**.
<br>
The **heatmap.2** function from the **gplots** package allows to produce highly customizable heatmaps.

```{r, eval=F}
# install pheatmap package
install.package("pheatmap")
```

Get started:

```{r, eval=T, results="hide"}
# load package
library(pheatmap)

# create matrix
mat <- matrix(rnorm(1200), ncol=6)

# heatmap with the defaults parameters
pheatmap(mat)

# add a title
pheatmap(mat, main="My pretty heatmap")
```

Change the color palette / gradient

```{r, eval=T}
# with "rainbow" colors
pheatmap(mat, 
         color=rainbow(50))

# with blue to red (middle color white)
pheatmap(mat, 
         color=colorRampPalette(c("navy", "white", "red"))(50))
```

Do not cluster rows or columns

```{r, eval=T, results="hide"}
# remove the clustering by rows
pheatmap(mat, 
         cluster_rows=FALSE)

# remove the clustering by columns
pheatmap(mat, 
         cluster_cols=FALSE)

# remove both clusterings
pheatmap(mat, 
         cluster_rows=FALSE, 
         cluster_cols=FALSE)
```

Add some **annotation colored bar(s)**:

```{r, eval=T}
# add column names to mat
colnames(mat) <- paste0("Sample", 1:6)

# create data frame for annotation (in the case of samples, information about the experiment, for example)
annot_cols = data.frame(
                Group = c(rep("WT", 3), rep("KO", 3)), 
                TimePoint = rep(c(0, 5, 10), each=2),
		            row.names = colnames(mat)
                )
# plot
pheatmap(mat, 
         annotation_col = annot_cols)
```

## venn.diagram function from VennDiagram package

*A Venn diagram shows all possible logical relations between data sets.*
<br>
The **venn.diagram** function from the **VennDiagram** package allows to create up to a 5-way Venn Diagram (i.e. 5 circles representing 5 data sets).

```{r, eval=FALSE}
# load package
library(VennDiagram)

# Prepare character vectors
v1 <- c("DKK1", "NPC1", "NAPG", "ERG", "VHL", "BTD", "MALL", "HAUS1")
v2 <- c("SMAD4", "DKK1", "ASXL3", "ERG", "CKLF", "TIAM1", "VHL", "BTD", "EMP1", "MALL", "PAX3")
v3 <- c("PAX3", "SMAD4", "DKK1", "MALL", "ERG", "CDKN2A", "DENR", "NPC1", "NAPG")

# Create a list of vectors
vlist <- list(v1, v2, v3)
names(vlist) <- c("list1", "list2", "list3")

# 2-way Venn
venn.diagram(vlist[1:2], 
	filename="Venn_2way.png",
	imagetype="png")
```

<img src="images/plots/Venn_2way.png" width="450"/>

```{r, eval=FALSE}
# 3-way Venn
venn.diagram(vlist, 
        filename="Venn_3way.png",
        imagetype="png")
```

<img src="images/plots/Venn_3way.png" width="450"/>

* More arguments:
	* main : title
	* sub : sub-title
	* main.col : color of title font
	* fill : color of circles
	* col : color of circle lines
	* cat.col : color of category labels

```{r, eval=FALSE}
venn.diagram(vlist,     
        filename="Venn_3way_more.png",
        imagetype="png",
	main="Venn diagram",
	sub="3-way",
	main.col="red",
	fill=c("lightgreen", "lightblue", "lightsalmon"),
	col=c("lightgreen", "lightblue", "lightsalmon"),
	cat.col=c("green", "blue", "salmon"))

```

<img src="images/plots/Venn_3way_more.png" width="500"/>