In marionlouveaux/cellviz3d: Tools for 3D/4D interactive visualization of cells and biological tissues

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Visualisation of a single mesh

The data in the example below were created with the package {mgx2r}, on the example dataset of {mgx2r}. This dataset is a timelapse recording of the development of a shoot apical meristem of the plant \emph{Arabidopsis thaliana} expressing a membrane marker. I took one 3D stack every 12h and have 5 timepoints in total. To know more about the example dataset of {mgx2r}, see the readme of {mgx2r}.

myMesh <- readRDS(system.file("extdata",
                              "mgx/mesh_meristem_full_T0.rds",
                              package = "cellviz3d"))

myCellGraph <- readRDS(system.file("extdata",
                                   "mgx/cellGraph_meristem_full_T0.rds",
                                   package = "cellviz3d"))

plotlyMesh() creates a {plotly} graph of type mesh 3D, with custom colors and custom hover information for a single mesh. Below, the mesh is displayed with one color and one cell label per biological cell. Cell label is visible only when hovering over the cell center. plotlyMesh() can be combined with show_tensors() and/or show_cellcontour().

meshCellcenter <- myCellGraph$vertices[,c("label","x", "y", "z")]

plotlyMesh(meshExample = myMesh,
           meshColors = myMesh$allColors$Col_label,
           meshCellcenter = meshCellcenter) %>%
  layout(scene = list(aspectmode = "data"))

silent <- file.copy(
  system.file("extdata", "mgx/img/p1labels.png", package = "cellviz3d"),
  "p1labels.png")
knitr::include_graphics("p1labels.png")

Visualisation of a time serie

The data in the example below were created with the package {mgx2r}, on the example dataset of {mgx2r}. This dataset is a timelapse recording of the development of a shoot apical meristem of the plant \emph{Arabidopsis thaliana} expressing a membrane marker. I took one 3D stack every 12h and have 5 timepoints in total. To know more about the example dataset of {mgx2r}, see the readme of {mgx2r}.

mesh.all <- readRDS(system.file("extdata",
                              "mgx/mesh_meristem_full_all.rds",
                              package = "cellviz3d"))

cellGraph.all <- readRDS(system.file("extdata",
                                   "mgx/cellGraph_meristem_full_all.rds",
                                   package = "cellviz3d"))

plotlyMesh_all() creates a plotly graph of type mesh 3D with a slider for a serie of meshes.

meshColors.all <- list(NULL, NULL, NULL, NULL, NULL)

plotlyMesh_all(meshExample = mesh.all,
                       graphExample = cellGraph.all,
                       meshColors = meshColors.all,
                       display = 'heatmap')

silent <- file.copy(
  system.file("extdata", "mgx/img/timeserie800ms.gif", package = "cellviz3d"),
  "timeserie800ms.gif")
knitr::include_graphics("timeserie800ms.gif")

For more examples, see the vignette of the {mgx2r} package:

devtools::install_github("marionlouveaux/mgx2r", build_vignettes = TRUE)
vignette("vignette_basics", package = "mgx2r")
vignette("vignette_time_series", package = "mgx2r")

marionlouveaux/cellviz3d documentation built on May 20, 2019, 9:55 a.m.