add synthetic data

Author: jtanevski

.gitignore

@@ -42,7 +42,6 @@ rsconnect/
 .DS_Store
 
 #other folders
-data/
 inst/doc
 doc
 Meta

R/data.R

@@ -0,0 +1,31 @@
+# MISTy companion data
+# Copyright (c) 2020 Attila Gabor
+
+#' Synthetic benchmark data for MISTy
+#' 
+#' Data generated from 10 random layouts of four cell types and empty space on 
+#' 100-by-100 gridby simulating a two-dimensional cellular automata model that 
+#' focuses on signaling events. Cell growth, division, motility and death are 
+#' neglected. The intracellular processes involve two layers, first the ligand 
+#' activation of signaling hubs and ligand production/secretion regulated by 
+#' proteins. The model simulates the production, diffusion, degradation and 
+#' interactions of 11 molecular species. Ligands are produced in each cell-type 
+#' based on the activity level of their production nodes and then freely diffuse, 
+#' degrade or interact with other cells on the grid. Other molecular species 
+#' involved in signaling are localised in the intracellular space and their 
+#' activity depends on ligand binding and intracellular wiring.
+#' 
+#' @format A named \code{list} of length 10. Each list item is a \code{tibble} that
+#' corresponds to a simulation of one random layout with information about each 
+#' cell in rows described by the following 14 variables:
+#' \describe{
+#'  \item{row, col}{location of the cell on the grid}
+#'  \item{ligA, ligB, ligC, ligD}{expression of ligands}
+#'  \item{protE, protF}{expression of intracellular proteins}
+#'  \item{prodA, prodB, prodC, prodD}{expression of regulatory proteins}
+#'  \item{type}{cell type id}
+#' }
+#' 
+#' 
+#' @source \url{https://github.com/saezlab/misty_pipelines/}
+"synthetic"

data/synthetic.rda

@@ -3,7 +3,7 @@ pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
   MISTy: MISTy.html
-last_built: 2021-03-30T09:08Z
+last_built: 2021-03-30T13:43Z
 urls:
   reference: https://saezlab.github.io/misty/reference
   article: https://saezlab.github.io/misty/articles

docs/pkgdown.yml

@@ -54,6 +54,9 @@
   <url>
     <loc>https://saezlab.github.io/misty/reference/run_misty.html</loc>
   </url>
+  <url>
+    <loc>https://saezlab.github.io/misty/reference/synthetic.html</loc>
+  </url>
   <url>
     <loc>https://saezlab.github.io/misty/articles/MISTy.html</loc>
   </url>