visustat_frame: visustat_frame

In grrchrr/VisuStatR: Visualizing Statistics on Images in R

visustat_frame

Description

With visustat_frame, continuous and discrete parameters can be mapped individually on color, shape and size for one timepoint.

Usage

visustat_frame(df, ...)

Arguments

df	dataframe of the form: df(track, time, X, Y, (Z,) mapping_parameters, ...)
image	character: filename of image
stack	logical: default: FALSE, single image file provided if time-resolved imagestack is used, set: TRUE
image.depth	numeric: set image bit-depth; just important if Z-projections are calculated
image.normalize	logical: normalize image
frame	integer: frame to be mapped
tracks	vector: defining tracks to be displayed
par.map	character: specifying parameter in df to be visualized by color
par.shape	character: specifying parameter in df to be mapped on shape
par.display	display option for mapping; default: TRUE, mapping is disable with: FALSE
par.max	numeric: defining upper range of color mapping
par.min	numeric: defining lower range of color mapping
par.unit	character: unit of the numeric mapped parameter
crop	logical: option for cropping images; default: FALSE
sub.img	logical: option for creating sub-images from specified tracks or pre-filtered df; default: FALSE
sub.window	numeric: size of the sub-images in pixels
sub.col	numeric: number of columns in which sub-images are arranged
tracks.size	numeric: size of tracks
tracks.alpha	numeric: transparency of tracks
tracks.length	numeric: length of tracks (in frames)
tracks.label	logical: when sub.img is used, display or hide track label
tracks.label.x	numeric: when sub.img is used, set x-position of label
tracks.label.y	numeric: when sub.img is used, set y-position of label
points.size	numeric: size of points
points.alpha	numeric: transparency of points
points.stat	character: display statistic; default: 'echo', for blurring; without blurring 'identity'
points.shape	numeric: set shape from ggplot2 shape palette
axis.tick	numeric: axis ticks in px
axis.display	logical: display axis
axis.labs	logical: display labs
unit	character: setting name of unit; default: 'px'
scaling	numeric: scaling factor for unit; default: 1
dimensions	numeric: specify whether the images are 2D or 3D. If 3D is selected the data is assumed to be in the form: df(track, time, X, Y, Z, mapping paramters, ...)
manual.z	numerice: specify Z-plane to be visualized if no projection or sub windows are used
scale.bar	logical: show scalebar; default: FALSE
scale.width	numeric: width of scalebar; default: 40
scale.height	numeric: height of scalebar; default: 10
scale.x	numeric: distance from left border of the image towards scalebar
scale.y	numeric: distance from bottom border of the image towards scalebar
scale.color	character: specify color from R-color palette or hexcode
interactive	logical: return the plot as an interactive plotly object. Not supported when using sub.img or crop modes.

Value

returns a ggplot2 plot-object which can be further modified

Examples

# import hiv motility tracking data
data('hiv_motility')
# get image files
images <- hiv_motility_images()
# run visustat_frame with default settings
visustat_frame(hiv_motility, image=images[15], frame=15, image.normalize=1)
# run visustat_frame with specified settings
visustat_frame(hiv_motility,
   image = images[15],
   frame = 15,
   tracks = c(48, 66, 102, 108),
   sub.img = TRUE,
   sub.col = 2,
   sub.window= 300,
   par.map ='speed',
   par.shape ='type',
   points.size=2,
   image.normalize=1
 )
# import clonogenic assay colony growth data
data('clonogenic_assay')
# get image files
images <- clonogenic_assay_images()
# run visustat_frame with default settings
visustat_frame(clonogenic_assay, image=images[15], frame=15, tracks.length=0, axis.display=0)

# import subcellular particle data
data('subcellular_particle_dynamics')
# get image files
images <- subcellular_particle_dynamics_images()
visustat_frame(subcellular_particle_dynamics,
 image=images[2], frame=2,
 tracks.length=0,
 axis.display=0,
 par.map='MEAN_INTENSITY') + scale_color_viridis_c(option='plasma')

grrchrr/VisuStatR documentation built on April 25, 2022, 11:30 a.m.