# Gallery

### Histogram of alignment scores

Assuming a single library loaded in a data frame called *clonotypes* with the `read clonotypes()`

function:

hist(log(clonotypes$score)

### Scale-free distribution of the clonotype expression levels

Assuming table *a* of clonotype counts produced with the `clonotype table()`

function, the following
commands study the first library in that table.

```
library(vegan)
plot(radfit(a?1), log="xy")
```

### Grouping libraries by bootstraped hierarchical clustering

Assuming table *a* of clonotype counts produced with the `clonotype table()`

function, containing six libraries (for instance two biological triplicates).

library(pvclust) plot(pvclust(a, n=1000))

### Differential expression analysis

Assuming table *a* of clonotype counts produced with the `clonotype table()`

function, containing six libraries (for instance two biological triplicates).

This representation is similar to *MA plots* used in microarray and digital expression analysis, where the *x* axis represents the average expression strength, and the *y* axis represents the fold change (both on a logarithmic scale). Black dots represent clonotypes over-represented in one population compared to the other.

library(edgeR) a.dge <- DGEList(counts=a,group=c("B","A","A","B","A","B")) a.dge <- estimateTagwiseDisp(DGEList(counts=a,group=c("B","A","A","B","A","B"))) a.dge.com <- exactTest(a.dge) detags <- function (COMPARISON, ADJUST="fdr", P=0.05, SORTBY="PValue", DIRECTION="all") { if (DIRECTION == "all") { significant <- ! decideTestsDGE(COMPARISON, adjust.method=ADJUST, p.value=P) == 0 } if (DIRECTION == "up") { significant <- decideTestsDGE(COMPARISON, adjust.method=ADJUST, p.value=P) > 0 } if (DIRECTION == "down") { significant <- decideTestsDGE(COMPARISON, adjust.method=ADJUST, p.value=P) < 0 } significant <- COMPARISON$table[significant,] significant <- significant[order(significant[,SORTBY]),] rownames (significant) } plotSmear(a.dge.dedup, allCol="grey", lowCol="grey", deCol="black", de.tags=detags(a.dge.com))