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A package for arbuscular mycorrhyzal fungi colonization

Home Page: https://mchiapello.github.io/Ramf/

R 100.00%

r-package arbuscular mycorrhizal fungi colonization grid-system trouvelot

ramf's Introduction

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 People

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ramf's Issues

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???

New types of plot

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

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

Grid Barplot

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

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

Split the Boxplot into 2 plots

Only points => new plot called dotplot
Reduce the focus on the dots in the current boxplot

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

Function to implement

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

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")

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?

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

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?]

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

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