iSEE custom panel

• Check extending iSEE at https://isee.github.io/iSEE-book/ for more details on the procedure to extend iSEE classes.

ReducedDimensionCoexpression

• Extension of the ReducedDimensionPlot of the core iSEE package.
• Allow to plot the expression and co-expression of two genes on a reduced dimension plot.
• Expression level of gene A and gene B are normalized between 0 and 1 and their level of expression is represented in shade of orange (geneA) and cyan (geneB).
• Cells expressing gene A and gene B (at a minimal threshold, defined by user) are represented in purple.
• Cells expressing not expressing any of the two genes are repsented with a small point, genes expression either gene A or gene B are represented with a medium size will cells expression both genes are represented with a big point.

Deploy the app

library(iSEE)

sce <- ... # load singlecell object

# Coloration according to two gene: 
source('ReducedDimensionCoexpression.R')

initgeneA <- "MLL-AF9"
initgeneB <- "Ikzf2"

RedDim2genes1 <-
  new("RedDim2genes",
      Type = "TSNE",
      XAxis = 1L, YAxis = 2L, geneA = initgeneA, geneB = initgeneB,
      PanelHeight = 900L, PanelWidth = 8L)

app = iSEE(sce, initial=list(RedDim2genes1))