plotObjects: Create plots similar to createPlotList using intracellular...

In vrrenske/shinyspots: Visualization and Analysis of Bacterial Cell Segmentation and Fluorescence Data

Create plots similar to createPlotList using intracellular object outlines instead of points.

Description

Plot projection of fluorescent objects inside cells in one or more cell groups based on cell length.

Usage

plotObjects(obdat,
            meshdat,
            groups = 1,
            cellcolor = "black",
            objectcolor = "green",
            transparency = 0.1,
            getdata = FALSE)

Arguments

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.

Value

A ggplot of cell and object projections showing the relative localization of the intracellular objects, grouped by cell length.

Author(s)

Renske van Raaphorst

See Also

createPlotList

Examples

## 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)

vrrenske/shinyspots documentation built on Oct. 28, 2023, 12:26 p.m.