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flowjotter

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Flowjotter is a time-saving tool for researchers working with High Dimensional Flow Cytometry data.

• Useful for quick, automated plotting of Cytometry data from the FlowJo data export table exported into excel files.

• Extremely fast conversion to Prism file format for users who would prefer to make their graphs or statistics in Prism (.prism files require Prism 10). If you have an earlier version of Prism, you can manually correct the file format to .pzfx

<figure> <img src="inst/logos/flowjotter_app.png" alt="The flowjotter UI" /> <figcaption aria-hidden="true">The flowjotter UI</figcaption> </figure>

Installation

You can install the development version of flowjotter from GitHub with:

if(!require(devtools)) {
  install.packages("devtools")
} 
devtools::install_github("SameOldSamOld/flowjotter")

.rs.restartR()

Running flowjotter

This is a basic example which shows you how to use the shiny app:

# Load Package
library(flowjotter)

# Run shiny app
flowjotter()

Usage

Choosing Graph types

Graph type is decided by the first character of the column title:

• % = Percentage Graph

• N = Number Graph

• M = MFI Plot

Red columns in the ‘Info Page’ table viewer highlight columns not starting with “%”, “N”, or “M”.

Column names must be unique.

Choosing Groups

The left-most column (‘Samples’) dictates groups for samples.

Everything before the first underscore (_) becomes grouped.

There is no limit on the number of groups

FAQ

Is there an example of how to setup an Excel file?

A typical Excel counts layout can be read in /data/ with base::load(), or downloaded in the flowjotter app Info Page.

Can my excel file contain multiple sheets?

Yes, but each sheet must have a consistent and viable column name, group name and data.

No:

• If you are changing the groups that are to be plotted in each sheet, it will not work.

• Groups must stay the same throughout the excel sheet e.g. HDM vs Nb vs Ca

• To perform multiple comparisons e.g. (HDM vs Nb) & (HDM vs Ca) & (Nb vs Ca), you will need to create multiple excel files

  • If multiple sheets are encountered, you may reach a warning if not correctly formatted.

Why are my images squished?

You may need to increase the ‘Height px’ or ‘Width px’ of your image

Why are my groups getting oversplitting into multiple groups?

Carefully read the figure legend, there is most likely a tiny typo in your Samples column.