visumot_all: visumot_all

In grrchrr/VisumotR: Visualizing Motility on Images

Description

Creates time-resolved images series of tracking data with modifiable parameter mapping. visumot_all is a wrapper function for visumot_frame and visumot_summary. User parameters for both functions can be passed via the lists visumot_frame.list and visumot_summary.list.

Usage

visumot_all(
  df,
  images,
  stack = FALSE,
  frame_range = NULL,
  display_frame = TRUE,
  display_summary = FALSE,
  visumot_frame.list = NULL,
  visumot_summary.list = NULL,
  save = TRUE,
  file_name = NULL,
  width = 2000,
  height = 1200,
  rel_width = 0.66,
  browse = FALSE,
  return = FALSE
)

Arguments

df	dataframe of the form: df(track, time, X, Y, mapping_parameters, ...)
images	vector: filenames of images ordered by frames/time
frame_range	integer: frames to be mapped; default=NULL maps full time/frame range found in df
display_frame	logical: display output from visumot_frame
display_summary	logical: display output from visumot_summary
visumot_frame.list	list: parameters passed to visumot_frame
visumot_summary.list	list: parameters passed to visumot_summary
save	logical: saves tiff-stack or image to ./output/visumotr-date.tiff
width	numeric: width of output tiff in pixels
height	numeric: height of output tiff in pixels
rel_width	numeric: if(display_frame & display_summary), rel_width defines the relative width of the summary plot to the mapped frame
browse	logical: browse output with default system application for tiffs, e.g. imageJ
return	logical: return images-series as magick image-stack

Details

To be written...

Examples

# import tracking data
df <- read.csv('hiv_tracking.csv')
# get image files
images <- list.files(pattern='.tif')
# run visumotR with default settings
visumot_all(df, images)
# run visumotR with visumot_frame and visumot_summary
tracks <- c(34, 125, 199, 205)
summary_pars <- list(par.map='angle', time.unit='min', tracks=tracks)
frame_pars <- list(par.map='angle', par.shape='infected', tracks=tracks)
visumot_all(df,
 images,
 frame_range = c(20,100),
 display_summary = 1,
 visumot_frame.list = frame_pars,
 visumot_summary.list = summary_pars,
 file_name = 'hiv_tracking_angle'
 )

grrchrr/VisumotR documentation built on March 3, 2021, 11:15 a.m.