View source: R/objectplotting.R
plotObjects | R Documentation |
Plot projection of fluorescent objects inside cells in one or more cell groups based on cell length.
plotObjects(obdat,
meshdat,
groups = 1,
cellcolor = "black",
objectcolor = "green",
transparency = 0.1,
getdata = FALSE)
obdat |
Object dataset "object_relative" as it is extracted using one of the "extr_"-functions. |
meshdat |
A mesh dataset as it is extracted using one of the "extr_"-functions (optional). |
groups |
The amount of groups to devide the cell projections in (by cell length). Default = 1. |
cellcolor |
The color of the cells in the cell projections. Default = black. |
objectcolor |
The color of the objects in the projections. Default = green. |
transparency |
The transparency of the objects and cells in the overlay. Default = 0.1. When analyzing ~1000 cells, it is advised to set this number to ~0.02 or less. |
getdata |
When getdata==TRUE, the function returns a dataset with the grouped cells next to the plot. Default is set to FALSE. |
A ggplot of cell and object projections showing the relative localization of the intracellular objects, grouped by cell length.
Renske van Raaphorst
createPlotList
## Not run:
#get objects & meshes from WT D39 cells stained with Van-FL, analyzed with oufti.
#download from https://veeninglab.com/f/example_datasets.zip
load("VanFL_meshWT")
load("VanFL_objWT")
#plot objects
plotObjects(VanFL_objWT, VanFL_meshWT, groups=4, transparency=0.1)
## End(Not run)
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