In epiviz/iSEEu.epiviz: Epiviz Genome Browser panel for iSEEu

knitr::opts_chunk$set(echo = TRUE)

Loading required packages

library(Homo.sapiens)
library(scRNAseq)
library(scater)
library(iSEEu.epiviz)

An example sce dataset

# Example dataset
sce <- ReprocessedAllenData(assays="tophat_counts")

set.seed(100)
sce <- logNormCounts(sce, exprs_values="tophat_counts")
sce <- runPCA(sce, ncomponents=4)
sce <- runTSNE(sce)
sce

Make a list of tracks

data("tcga_colon_blocks")
data("tcga_colon_expression")

browser <- EpivizBrowser(chr="chr11", start=118000000, end=121000000, genome=Homo.sapiens, tracks=list("tcga_peaks" = tcga_colon_blocks, "tcga_expression"=tcga_colon_expression), PanelWidth=12L, PanelHeight=400L)

Spin up iSEE with browser panel

app <- iSEE(sce, initial=list(
  ReducedDimensionPlot(Type="TSNE", VisualBoxOpen=TRUE, VisualChoices="Size", PanelWidth=6L),
  browser))
app

epiviz/iSEEu.epiviz documentation built on Dec. 20, 2021, 5:27 a.m.