mchiapello / ramf

A package for arbuscular mycorrhyzal fungi colonization

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.

ramf's Issues

Grid Barplot

I changed the order on x axis in commit 4cce9a7, but the plot are not correct!!
Fix the issue

Statistical analysis

Added statistical analysis to package

• How to do it?

• Table?

  • Directly into am_summary fx

• Plot?

  • Added stat analysis on plot? [how easy is it?]

Bug in plot with letters for analysis with more than 10 samples

If there are more than 10 samples the letters order on the plot is wrong -- thanks Julia Brandes to spot the bug

Letters and asterisks

It seems there is a problem in letters and asterisks on plots.
I fixed the letters. BUT letters and asterisks seem not to correspond!!
Double check

Trouvelot bug

summary trouvent contains a bug!!

• If the number of replicates is uneven, the script reports also for the samples without specific replicates, that replicates with NA

Coding Issue

I am using the trouvelot scoring method and keep running into an error that I am unsure how to fix. After running the am_stat function I receive "Error in if (pvalue[k] <= 0.001) sig[k] <- "***" else if (pvalue[k] <= :
missing value where TRUE/FALSE needed". I have tried many different combinations and attempted to look online but have had no look. Any advice how I can fix this?

New types of plot

After a long discussion, we decided to include also plots with legends.
Working to add the new display

Function to implement

• summary for class trouvelot => summary table
• summary for class grid => summary table

GRID SYSTEM

The grid system fx is NOW working only with all the 7 columns!!!

The grid class SHOULD BE RE_WROTE in order to work also with some missing scoring columns

Cannot load csv into data frame to "readData()"

I formatted my csv in the format suggested and cannot get R to load the data to even do the readData() function. I have tried different ways of selecting the csv file and variations of the recommended code from https://www.frontiersin.org/articles/10.3389/fpls.2019.01184/full#f1 but none of it has been working for me. The csv downloads as a value that says "character empty" instead of the 7-column data frame that I would expect. When I use this code: Ramf.data<-read.csv(file.choose()) I can see the data in a data frame, but then when I go to do any actions in the Ramf package (including readData) I get this error message:

Error in vroom::vroom(): ! file is not one of the supported inputs: • A filepath or character vector of filepaths • A connection or list of connections • Literal or raw input Run rlang::last_trace() to see where the error occurred.
Backtrace: ▆

└─Ramf::readData((as.data.frame("Ramf5")), type = "grid")
├─base::suppressMessages(read_csv(infile))
│ └─base::withCallingHandlers(...)
└─readr::read_csv(infile)
└─vroom::vroom(...)
Run rlang::last_trace(drop = FALSE) to see 3 hidden frames.

I want to look at the data frame using readData() and use the other functions in Ramf as well, but I can't use the actions without the mentioned error message. Here is what I have for code so far (that has not been working):

#Ramf Ramf.data<-read.csv(file.choose()) Ramf.6 <- dir(system.file("Ramf.csv", package = "Ramf"), full.names = TRUE, pattern = "grid.csv") readData((as.data.frame("Ramf.data")), type="grid") readData(Ramf.6, type="grid")

Split the Boxplot into 2 plots

• Only points => new plot called dotplot

• Reduce the focus on the dots in the current boxplot

Validation

replicates column MUST be character and not numeric:

• Add a validation step

• Add a test unit

If is numeric the dataset should be NOT import or the column converted to character???

validation 2

scoring column SHOULD not contain 0.

• Add validation

• Add test unit

if the column contains 0, the dataset should be rejected or the 0 should be converted into 0A0

trouvelot verification

Add verification to trouvelot:

• Now column scoring can accept values out of 0A0, 0A1, ... 5A3

• readData should throw an error if in scoring column there are not acceptable variables