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Plotting Genealogy

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vrrenske edited this page Oct 18, 2019 · 6 revisions

Plotting Genealogy

Goal

In this short tutorial I’ll show how to use BactMAP to convert your SuperSegger or Oufti genealogy data into tree plots. While the other functions of BactMAP generate complete (though changeable) plots, the tree plotting is a little different. While I plan to automate the plots further in the future, now this requires a little more coding on the user side. This tutorial aims to help you use BactMAP along with the ggtree package for plotting the networks of cells, and use the ggplot-functionalities to change the appearance of the plot the way you want.

Contents

  1. Before Getting Started
  2. Data Import
  3. Exploring the Data Structure
  4. Plotting Basic Trees
  5. Plotting Trees & Fluorescence Data
  6. More Tree Manipulation
  7. Using Other Packages
  8. Resources
⬅️ Tutorials Overview ▪️ ◾ ▪️ Genealogy Part 1: Before Getting Started ➡️

Getting Started

  1. Download & Install
  2. Tutorials
  3. General Workflow

Data Import & Conversion

  1. Import Data
  2. Add Localization to Segmentation
  3. Combine Conditions & Channels
  4. Saving Data

Plotting

  1. Overview
  2. Using TIFFs
  3. Localization
  4. Timelapse

Utilities

  1. Color Palettes
  2. Pixel-Micron Conversion
  3. Working with Large Data Sets
  4. Version Compatibility

Data Structure

  1. Mesh
  2. Spots
  3. Objects
  4. Raw Images
  5. Phylogeny
  6. cellList

Example Datasets

  1. Example Dataframes
  2. Origin Localization
  3. Time-Lapse of DnaX and FtsZ
  4. Comparing Segmentations 1
  5. Comparing Segmentations 2

Contact us

  1. Report an issue
  2. email
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