Configuring iSEE apps

Kevin Rue-Albrecht1*, Federico Marini2,3**, Charlotte Soneson4,5*** and Aaron Lun****

1MRC WIMM Centre for Computational Biology, University of Oxford, Oxford, OX3 9DS, UK
2Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz
3Center for Thrombosis and Hemostasis (CTH), Mainz
4Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
5SIB Swiss Institute of Bioinformatics

*kevinrue67@gmail.com
**marinif@uni-mainz.de
***charlottesoneson@gmail.com
****infinite.monkeys.with.keyboards@gmail.com

Package

iSEE 2.19.3

Compiled date: 2025-03-06

Last edited: 2020-04-20

License: MIT + file LICENSE

1 Changing the default start configuration

The default start configuration with one plot of each type may not always be the most appropriate. iSEE allows the user to programmatically modify the initial settings (Rue-Albrecht et al. 2018), avoiding the need to click through the choices to obtain the desired panel setup. Almost every aspect of the initial app state can be customized, down to whether or not the parameter boxes are open or closed!

To demonstrate this feature, let’s assume that we are only interested in feature assay plot panels. The default set of panels can be changed via the initialPanels argument of the iSEE function call. Given a SingleCellExperiment or SummarizedExperiment object named sce111 We’ll re-use the example from the previous workflow., the following code opens an app with two adjacent feature assay plots. Note that each panel is set to occupy half the width of the application window, which is set to 12 units by the shiny package.

library(iSEE)
app <- iSEE(sce, initial=list(
    FeatureAssayPlot(PanelWidth=6L),
    FeatureAssayPlot(PanelWidth=6L)
))

The genes to show on the Y-axis in the two plots can be specified via the YAxisFeatureName argument to the respective panels in iSEE.

app <- iSEE(sce, initial=list(
    FeatureAssayPlot(YAxisFeatureName="0610009L18Rik"),
    FeatureAssayPlot(YAxisFeatureName="0610009B22Rik")
))