https://github.com/vrrenske/BactMAP

gateway for segmentation data to Rstats & visualization with ggplot2 - in development
https://github.com/vrrenske/BactMAP

fluorescence-data ggplot visualization

Last synced: 28 days ago
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gateway for segmentation data to Rstats & visualization with ggplot2 - in development

• Host: GitHub
• URL: https://github.com/vrrenske/BactMAP
• Owner: vrrenske
• License: other
• Created: 2016-10-04T15:18:16.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2023-10-24T14:31:41.000Z (about 1 year ago)
• Last Synced: 2024-08-04T00:13:02.599Z (4 months ago)
• Topics: fluorescence-data, ggplot, visualization
• Language: R
• Homepage: http://veeninglab.com/
• Size: 121 MB
• Stars: 4
• Watchers: 1
• Forks: 4
• Open Issues: 5
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Awesome Lists containing this project

• awesome-biological-image-analysis - BactMap - A command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots. (Microbiology)

README

        
---

title: "BacTMAP"

output:

  github_document:

    fig_width: 2

    fig_height: 2

    

---

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)

library(bactMAP)

```

## BacTMAP - Bacteria Tool for Microscopy Analysis & Plotting



This package is meant to make it easier for microbiologists to combine and analyse segmentation & fluorescence data derived from custom software like Oufti, Morphometrics, MicrobeJ or Supersegger. There are standard functions for importing several popular programs, but also options for importing CSVs or Matlab files with a specific structure. If your favorite segmentation or spot detection program is missing, don't hesitate to ask!

I use ggplot and many ggplot-extensions to make visual summaries of the segmentation & fluorescence data, show the cell genealogy, plot protein trajectories in the cell and many other things. This can give you a quick overview of your data to make a decision on further analysis and custom visualization.

In the [wiki](https://github.com/vrrenske/BactMAP/wiki) you will find a manual and some examples on how to use BactMAP as a gateway between your segmentation & fluorescence data.

**BactMAP is still in development. Not all functions listed below are fully tested & documented yet. If you have any comments, requests, please let me know!**

## Download and install package

```

#install devtools if not done yet

install.packages("devtools")

#install bactmap from my github repository

devtools::install_github("vrrenske/bactMAP")

#or install it with all dependencies

devtools::instal_github("vrrenske/bactMAP", dependencies=TRUE)

#load package

library(bactMAP)

```