extr_Oufti: Function to import Oufti data.

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

Function to import Oufti data.

Description

Import oufti meshes, objects and spot localizations directly from .Mat, .txt or .CSV files to R. Note that oufti objects can only be imported from .csv or .txt files.

Usage

extr_Oufti(matfile, mag="No_PixelCorrection", phylo=FALSE, cellList=FALSE)

Arguments

matfile	.MAT, .CSV or .TXT of oufti segmentation. Spot data, object data and fluorescence intensity will automatically be detected. Note: object data can only be extracted from .CSV or .TXT files for now!
mag	The pixel-micron conversion factor. See bactMAP::getPixels2um() for more information. When not given, the factor will be 1.
phylo	When TRUE, a list of child-parent nodes & phylo objects containing cell genealogy will be made. Takes very long, so default is set to FALSE
cellList	When TRUE, the cellList (see Value below) will be part of the output list.

Value

A list containing:

$cellList	The complete cellList as it is displayed in oufti's output.
$mesh	A dataframe containing the following columns: X, Y, cell, frame, num, max.width, length, steplength, max.length, area, Xmid, Ymid, X_rot, Y_rot, angle, Xrot_micron, Yrot_micron, max_um, maxwum. See standard mesh output for more information.

When spot data is included:

$spotframe	A dataframe containing the following columns: l, d, x, y, position, adj_Rsquared, CI_xy, frame, cell. See www.oufti.org for more information on the spot data output.
$spots_relative	A dataframe containing from the mesh data: max.width, max.length, area, cell, frame. from the spot data: l, d, x, y. Added: spot, totalspot, Lmid, Dum, max_um, maxwum, pole1, pole2.
$pixel2um	the pixel to micron conversion factor used

When a CSV or TXT file containing object data:

$objectframe	A dataframe containing the coordinates of detected objects, cell ID, frame ID and object ID: ob_x, ob_y, obnum, obpath, frame, cell, obID
$object_relative	A dataframe reminescent of spots_relative containing the following variables: "frame, cell, max.length, obnum, num, obpath, obID, max.width, Dum, Lmid, ob_out_x, ob_out_y, pole1, pole2

When "phylo" is set to TRUE:

$timelapsedata

a list of: generation_dataframes: a dataframe with cells with common ancestor, generation_lists: phylo objects which can be used for tree plotting, spot_relative_list: list of spot localization dataframes of cells with common ancestor, and meshdata: a list of cell outline data of cells with common ancestor

Author(s)

Renske van Raaphorst

References

www.oufti.org

Paintdakhi A, et al. (2016) Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis. Molecular Microbiology 99(4):767-777.

Examples

## Not run: 
##upload matlab oufti file
matfile <- file.choose()
##extract data using extr.Oufti()
output <- extr_Oufti(matfile)
##get spot dataframe
spots <- output$spotframe
##plot spots of frame no.1
ggplot2::ggplot(spots[spots$frame==1,],
    ggplot2::aes(x=x, y=y, color=as.factor(cell))) +
  ggplot2::geom_point() +
  ggplot2::theme_minimal()

## End(Not run)

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