In ddiez/q3tools: A bunch of shabby tools for the omics data analyst

Introduction

Required packages for building this vignette:

knitr::opts_chunk$set(fig.width=5, fig.height=5)
library(q3tools)
library(dplyr)
library(Biobase)
library(IRanges)
library(GenomicRanges)

Dots plot

You can use matrices.

tmp1 <- data.matrix(iris[1:4, -5])
plotPoints(tmp1, group = rep(LETTERS[1:2], each = 2))

You can use other objects like ExpressionSet.

data(sample.ExpressionSet)
tmp2 <- sample.ExpressionSet[1:4, ]
plotPoints(tmp2, group = tmp2$sex)
plotPoints(tmp2, group = tmp2$type)

Histograms

A histogram.

plotHistogram(tmp1)
plotHistogram(tmp1, group = rep(LETTERS[1:2], each = 2))

An example using ExpressionSet object.

plotHistogram(tmp2)
plotHistogram(tmp2, group = tmp2$sex)
plotHistogram(tmp2, group = tmp2$type)

Pairs

A paired scatterplot.

plotPairs(mtcars[,1:4])

plotPairs(mtcars[,1:4], geom.low = "point", geom.mid = "density", geom.up = "density2d")

tmp <- matrix(rnorm(1000 * 4), ncol = 4)
plotPairs(tmp, geom.low = "hex", geom.up = "density2d")

Heatmaps

A heatmap.

tmp2 <- sample.ExpressionSet[1:25, ]
plotHeatmap(tmp2)
plotHeatmap(tmp2, col.cluster = TRUE, scale = TRUE)

A correlation heatmap.

plotCorrelation(exprs(sample.ExpressionSet), cluster = TRUE)

Venn diagrams

A venn diagram.

plotVenn(
  iris[, -5] > 2,
  fill = c("cornflowerblue", "orange", "darkorchid1", "yellowgreen"),
  alpha = .3,
  col = NA
  )

MDS

A MDS plot.

plotMds(iris[, -5], group = c("A", "A", "B", "B"))

Gene tracks

A gene track.

# plot some gene.
plotGene("Stat1", "mm10")
# add some data.
f <- system.file("files/example.bam", package = "q3tools")
plotGene("Stat1", "mm10", add.data = list("Exo+" = f))
# zoom in.
plotGene("Stat1", "mm10", add.data = list("Exo+" = f), from = 52.12e6, to = 52.14e6)

The above code may fail if the genome version at Biomart differs from the version expected by Gviz, the underlaying package used by plotGene. In that case, the biomart object mast be specified directly. In that case, the argument genome is ignored.

library(biomaRt)
mart <- useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl")
f <- system.file("files/example.bam", package = "q3tools")
plotGene("Stat1", biomart = mart, add.data = list("Exo+" = f), from = 52.12e6, to = 52.14e6)

Ranges

A set of ranges.

tmp <- IRanges(start = c(1, 7, 10, 5, 13), end = c(4, 12, 15, 8, 14))
tmp
plotRanges(tmp, sep = .3)

If we have GRanges we have to specified the seqname.

# create GRanges from IRanges.
tmp <- GRanges(seqnames = c(1,1,2,2,2), ranges = tmp)
plotRanges(tmp, seqnames = "1")
plotRanges(tmp, seqnames = "2")
# override seqnames.
plotRanges(ranges(tmp))