makeApp: Make a shiny app to interactively explore data

In JEFworks-Lab/MERINGUE: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities

Make a shiny app to interactively explore data

Description

Make a shiny app to interactively explore data

Usage

makeApp(
  pos,
  gexp,
  results,
  title,
  description = NULL,
  pal = colorRampPalette(c("blue", "grey", "red"))(100),
  scale = TRUE,
  zlim = c(-1.5, 1.5),
  ...
)

Arguments

pos	Position
gexp	Gene expression
results	Dataframe of analysis results
title	Page title
description	Page description
pal	Color ramp palette
scale	Boolean of whether to scale and center expression values
zlim	Color range
...	Additional plotting parameters

Value

Shiny app

Examples

data(mOB)
pos <- mOB$pos
gexp <- as.matrix(normalizeCounts(mOB$counts, log=FALSE))
results <- mOB$results
results[, 1:3] <- round(results[, 1:3], digits=3)
makeApp(pos,
        gexp,
        results,
        title='mOB',
        description='Mouse Olfactory Bulb Spatial Transcriptomics Data')

JEFworks-Lab/MERINGUE documentation built on June 8, 2022, 11:41 p.m.