| Title: | Multiple Ploidy Estimation Tool for all Species Compatible with Flow Cytometry |
| Version: | 0.1.1 |
| Description: | A graphical user interface tool to estimate ploidy from DNA cells stained with fluorescent dyes and analyzed by flow cytometry, following the methodology of Gómez-Muñoz and Fischer (2024) <doi:10.1101/2024.01.24.577056>. Features include multiple file uploading and configuration, peak fluorescence intensity detection, histogram visualizations, peak error curation, ploidy and genome size calculations, and easy results export. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| Date/Publication: | 2025-01-15 19:40:19 UTC |
| RoxygenNote: | 7.3.2 |
| Imports: | BiocManager, dplyr, DT, ggplot2, ggrepel, gridExtra, markdown, shiny, shinythemes, tidyr, zoo |
| Suggests: | knitr, flowCore, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2025-01-15 16:07:57 UTC; cintia |
| Author: | Cintia Gómez-Muñoz
 [aut, cre],
Gilles Fischer
[aut] |
| Maintainer: | Cintia Gómez-Muñoz <cintia.gomez_munoz@sorbonne-universite.fr> |
| Repository: | CRAN |
Run the MuPETFlow app
Description
This function launches the Shiny app included in MuPETFlow. Once the application is launched, you can either:
Load your experimental data.
Run an in-app example by clicking the 'Example' button.
Notes: For the first case, selecting the channel where the data was acquired is mandatory. If you choose the second, the tool will download the example files in a temporary file. This process requires internet connection and might take a few minutes. Then, the example channel `FL4-A` is automatically detected for demonstration purposes.
Usage
runMuPETFlow()
Details
After launching the app, you can follow the app flow, which is divided into three tabs: Peaks, Regression and Summary. Below is a general description of the options available in each tab:
Peaks
-
Select a sample (optional): Allows visual exploration of individual samples if desired.
-
Adjust smoothing (optional): Adjusts the histogram curve for noisy samples.
-
Adjust window width (optional): Defines the interval where the app will look for peaks.
-
Select minimum cell count to call a peak (optional): Useful for samples with a low number of events.
-
Select maximum number of peaks to plot (optional): Useful for samples with heterogeneous populations where more peaks are present.
Regression
-
Select type of analysis: Choose between "Ploidy" or "Genome size" analysis.
-
Select number of standards: A minimum of two different standards is required, but more are recommended.
-
Select standard samples and values: This is the ploidy or genome size of your standards.
Summary
-
Results preview: Creates a compiled figure with histograms for all samples.
-
Save plot: Saves the histograms in either PNG or TIFF format with customizable size and quality. Optionally, you can control the grid layout.
-
Save table: Exports the parameters used and the estimated ploidy or genome size as a CSV file.
If any errors are detected in the analyzed samples, you can go back to the Peaks tab to review the parameters. Note that the regression must also be re-done after parameter adjustments.
Value
No return value, called for side effects.
Examples
if (interactive()) {
# Example: Check that the function exists and runs
runMuPETFlow()
} else {
message("This is a Shiny app wrapper. Run interactively to use.")
}