sebepedroslab/shinyscdb

This package contains functions for single-cell atlas database shiny apps, including single species metacell atlases and comparative anlyisis between pairs of species.

To use these functions, each app needs to have config.yaml in which input files are specified, and global.R (example below), with libraries and global variables, including list of species (the species acronyms should match those used in config file).

# packages
options(repos = BiocManager::repositories())
library(BiocManager)
library(shiny)
library(data.table)
library(dplyr)
library(reshape2)
library(stringr)
library(glue)
library(ggplot2)
library(ggpubr)
library(RColorBrewer)
library(viridis)
library(gplots)
library(shinydashboard)
library(shinyWidgets)
library(DT)
library(zoo)
library(kableExtra)
library(ComplexHeatmap)
library(circlize)
library(scales)
library(patchwork)
library(rtracklayer)
library(shinyscdb)
library(shinycssloaders)

# config file
conf <- yaml::yaml.load_file("config.yaml", eval.expr=TRUE)

# species dictionary with '"full name" = acronym' pairs
sps <- c(
  "Hoilungia hongkongensis" = "Hhon",
  "Trichoplax adhaerens" = "Tadh",
  "Nematostella vectensis" = "Nvec"
)

# graphical params
heatmap_colors <- c("white","gray99","orange","orangered2","#520c52")

# env interactive heatmap
shiny_env = new.env()