epistack 1.10.0
The epistack
package main objective is the visualizations of stacks
of genomic tracks (such as, but not restricted to, ChIP-seq or
DNA methyation data)
centered at genomic regions of interest. epistack
needs three
different inputs:
GRanges
(easily obtained from bigwig
or bam
files)GRanges
(easily obtained from gtf
or bed
files)Each inputs are then combined in a single RangedSummarizedExperiment
object use by epistack’s
ploting functions.
After introducing epistack’s plotting capacity, this document will present two use cases:
Epistack is a visualisation package. It uses a RangedSummarizedExperiment
object as input, with
matrices embeded as assays. We will discuss how to
build such input obects in the next section. For now on, we will focus on
the visualisation functions using the example dataset included in the package.
The dataset can be accessed with:
library(GenomicRanges)
library(SummarizedExperiment)
library(epistack)
data("stackepi")
stackepi
#> class: RangedSummarizedExperiment
#> dim: 693 51
#> metadata(0):
#> assays(1): DNAme
#> rownames(693): ENSSSCG00000016737 ENSSSCG00000036350 ...
#> ENSSSCG00000024209 ENSSSCG00000048227
#> rowData names(3): gene_id exp score
#> colnames(51): window_1 window_2 ... window_50 window_51
#> colData names(0):
plotEpisatck()
functionThis dataset can be visualised with the plotEpistack()
function.
The first parameter is the input RangedSummarizedExperiment
object.
The second (optionnal) parameter, assays
specifies which assay(s)
should be displayed as heatmap(s). In the stackepi
dataset, only one track is present, with an assay names DNAme
.
Note that it is possible to have several different tracks embeded in the
same RangedSummarizedExperiment
object, as demonstarted in the next sections.
An aditional metric_col
is used, to display score associated with each
anchor region, such as expression values or peak scores. Optionaly,
the metric_col
can be transformed before ploting using the
metric_transfunc
parameters.
plotEpistack(
stackepi,
assay = "DNAme", metric_col = "exp",
ylim = c(0, 1), zlim = c(0, 1),
x_labels = c("-2.5kb", "TSS", "+2.5kb"),
titles = "DNA methylation", legends = "%mCpG",
metric_title = "Expression", metric_label = "log10(TPM+1)",
metric_transfunc = function(x) log10(x+1)
)
If a bin
column is present, it is used to generate one average profile per bin.
stackepi <- addBins(stackepi, nbins = 5)
plotEpistack(
stackepi,
assay = "DNAme", metric_col = "exp",
ylim = c(0, 1), zlim = c(0, 1),
x_labels = c("-2.5kb", "TSS", "+2.5kb"),
titles = "DNA methylation", legends = "%mCpG",
metric_title = "Expression", metric_label = "log10(TPM+1)",
metric_transfunc = function(x) log10(x+1)
)
Colours can be changed using dedicated parameters:
plotEpistack(
stackepi,
assay = "DNAme", metric_col = "exp",
ylim = c(0, 1), zlim = c(0, 1),
x_labels = c("-2.5kb", "TSS", "+2.5kb"),
titles = "DNA methylation", legends = "%mCpG",
metric_title = "Expression", metric_label = "log10(TPM+1)",
metric_transfunc = function(x) log10(x+1),
tints = "dodgerblue",
bin_palette = rainbow
)