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:
Installation
For installation in RStudio download the package and follow the instructions below:
- Install the following packages:
- caroline
- gplots
- dunn.test
- RColorBrewer
To this end start RStudio, select
from the menu bar.“Tools” → “Install Packages…”
Choose
and enter the names of the packages.“Install from: Repository (CRAN)”
Activate“Install dependencies”.
- The multtest package can be installed via the following Bioconductor installation script:
source ("http://bioconductor.org/biocLite.R")
biocLite("multtest")
- Install the PaCeQuantAna package selecting
“Tools” → “Install Packages…”
from the menu bar.
Choose
and select the tar.gz file of PaCeQuantAna via“Install from: Package Archive File (.tgz; .tar.gz)"
"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.