Applications/PaCeQuantAna

PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues

We provide an R package for visualizing and analyzing features extracted by PaCeQuant.

Please note:
The new version compatible with PaCeQuant as released in MiToBo 2.0 in May 2020 will appear soon!
Due to implications of the Corona pandemic the release of the package update had to be postponed.
We apologize for the inconvenience and hope to be able to make the new PaCeQuantAna release available to you very soon.

The old version of PaCeQuantAna compatible with PaCeQuant results generated with MiToBo 1.8.x can be downloaded here:

• R package v1.0.0

Installation

For installation in RStudio download the package and follow the instructions below:

1. Install the following packages:
   • caroline
   • gplots
   • dunn.test
   • sm
   • RColorBrewer

   To this end start RStudio, select

   “Tools” → “Install Packages…”

   from the menu bar.
   Choose

   “Install from: Repository (CRAN)”

   and enter the names of the packages.
   Activate

   “Install dependencies”.

2. The multtest package can be installed via the following Bioconductor installation script:
   

   source ("http://bioconductor.org/biocLite.R")

   biocLite("multtest")

3. Install the PaCeQuantAna package selecting

   “Tools” → “Install Packages…”

   from the menu bar.
   

   Choose

   “Install from: Package Archive File (.tgz; .tar.gz)"

   and select the tar.gz file of PaCeQuantAna via

   "Browse...".

Documentation

Find more details of how to use the package and details about the general workflow in the vignette of the package by either navigating to the vignette in the Rstudio package manager tab or by typing

vignette("PaCeQuantAna")

in the console.

The vignette contains comprehensive documentation of the various functions and options of the package.
In addition, a sample workflow R script is provided which shows all commands to load your data, configure the output and do the analysis.
You can directly copy the script into a file and load this file into the Rstudio editor to run it completely or line-wise.

You can test the package on these sample data: sample data for PaCeQuantAna

Important notes

• By default the working directory (set with setpw(...)) where the result folder will be created, and the data directory (set with setDataDir(...)) must not be identical!
  If you require these folders to be identical for whatever reason you need to manually edit the file data_description.csv in the output folder and delete the row referring to the output folder.
• On Windows operating systems you may encounter problems with missing fonts, i.e., error messages like the following one:

  ...

  Error in pdf(file = paste0(outdir, fsep, base_file_name,

  "_dunn_test_heatmap_adjusted_pvalues.pdf"),  :

    unknown family 'Arial'

  ...

  To circumvent these problems call once in Rstudio the following two commands,

  library(extrafont)

  font_import()

  Initialize each of your workflows using PaCeQuantAna with

  library(extrafont)

  This will initialize the Windows font database and should solve the problems.