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Table of Contents¶

Table of Contents

Introduction to the step by step guide

Create Project

Preparation of the 3 files

Checking if all the annotation are correct

Create Filter

Customization of Plots

Download the Data and Plots

Introduction to the step by step guide¶

Here is a step by step instruction on how to run the FlowJo stat workflow.
It is a workflow allowing automation and parallelization of many plots analysis.

Create Project¶

Create a Project in Tercen
Note: If you create in a Team then you can share it easier

Preparation of the 3 files¶

You require three files

Measurement file
Sample annotation file
Display name file

These can be created from the Flowjo Export Table file

Here is a link to a template of the three files.
Download them and fill them.

Uploading the data¶

When uploading the data:

ATP import as “character”
SEB import as “character”
Days import as “character”

Finding the template¶

I copied it from a project

Open the workflow¶

Gather Step¶

Remove all and add all

Join Step¶

Run the join

Wizard Step¶

Question	Action	Remark
"Select the samples column from the measurement file (i.e., FlowJo file). Examples: `samples	samples	Had to select
"Select the samples column from the sample annotation file. Examples: `sample.samples`	sample.samples	Automatically selected
"Select the ELN column from the sample annotation file, otherwise, leave blank. Examples: `sample.ELN`",	sample.ELN	Had to select
No selection necessary, click Next	exp.variable	Automatically selected
No selection necessary, click Next	cellpop.Flowjo name	Automatically selected
No selection necessary, click Next	cellpop.Display name	Automatically selected
No selection necessary, click Next	Cell.pop Display name “NA” “ “	Automatically selected
No selection necessary, click Next	cell.pop.Display name “NA” “ “	Automatically selected
No selection necessary, click Next	exp.value	Automatically selected
"Select the factors representing the conditions. Multiple selections are possible. Examples: `sample.compound`, `sample.ATP`, `sample.Ab`, `sample.Ab2` and etc..",	sample.Ab sample.Ab2 sample.treatment sample.STP sample.SEB	Manually selected
Selecting the control per condition (z-score on mean) Filters - Select your control compound/condition	sample.treatment = DMSO ATP =0 SEB =1 Ab= PD1 Ab2 = Belrestotug	Manually selected Apply filter

Checking if all the annotation are correct¶

Checking if all there is one single value per cell

Create Filter¶

Customization of Plots¶

Point plot	2Gb
Barplot (mean) with jitter	2Gb
Barplot (mean) with sd error bars	2Gb
Heatmap	2Gb, 1000x3000