README.md

The Ramf package

A package for arbuscular mycorrhyzal fungi colonization

Citation

If you use the package, please cite it:

Marco Chiapello , Debatosh Das, Caroline Gutjahr. Ramf: An open-source R package for statistical analysis and display of quantitative root colonization by arbuscular mycorrhiza fungi. _Frontiers Plant Science_. **In press**.

Installation

devtools::install_github("mchiapello/Ramf")

If you get this error:

"ERROR: dependency 'BiocStyle' is not avalilable for package 'Ramf'"

Please, install the package from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BiocStyle")

Repeat the Ramf package installation command.

Simple usage

Read the Reference page for more information.

## Load library
library(Ramf)

## Read data in
f <- dir(system.file("extdata", package = "Ramf"), full.names = TRUE, pattern = "grid.csv")
x <- readData(f, type = "grid")

## Summary of the data
am_summary(x)

## Plot
am_barplot(x)
am_boxplot(x)
am_dotplot(x)

# Plot with different display
am_barplot2(x)
am_boxplot2(x)
am_dotplot2(x)

## Statistics
am_stat(x)
am_stat(x, methods = "BH")

## Plot with statistics
am_barplot(x, annots = "asterisks")

## Plot with statistics
am_barplot(x, annot = "letters")

## Save summary data
am_save(am_summary(x), "My_data") # 2 files will be save: "My_data_per_Sample.csv" and "My_data_per_Replicate.csv"

## Save plot data
am_save(am_dotplot(x), "RPlot.jpg")
am_save(am_dotplot(x), "RPlot.pdf", unit = "cm", width = 20, height = 20, dpi = 300) # set image unit, dimention and quality
am_save(am_dotplot(x), "RPlot.png", width = 7, height = 7)

If you encounter a bug, please report it on github.