How to plot figures?

[RemyMG]

Hello,

I'm running MetaboAnalystR 4.0.0 on R 4.3.1 in RStudio 2023.06.0 Build 421 and I don't know how to plot any figures. The code lines mSet <- PlotNormSummary(mSet, "norm_0_", "png", 72, width=NA) or mSet <- PlotFC(mSet, "fc_0_", "png", 72, width=NA) don't display any figure and this single code line PlotNormSummary(mSet, "norm_0_", "png", 72, width=NA) displays the whole mSet object in the console. So how can I get the plots in the RStudio "Plot" pane? Is it a bug from the MetaboAnalystR functions or is there something I'm not doing correctly?

I really thank you for your help.

Here are the codes lines from my console, with data from the tutorial:

`library(googledrive); temp <- tempfile(fileext = ".csv")

Download data

dl1 <- drive_download(as_id("1wEh2P81J_xFWJs5y4mq98-FsjxJ5wmBO"), path = temp, overwrite = TRUE) File downloaded: metaboanalyst_input.csv Saved locally as: /tmp/RtmpIBzO2x/file41dc1f662ed1.csv

Load data

mSet<-Read.TextData(mSet, "file41dc1f662ed1.csv", "colu", "disc") mSet<-SanityCheckData(mSet) [1] "Successfully passed sanity check!"
[2] "Samples are not paired."
[3] "3 groups were detected in samples."
[4] "Only English letters, numbers, underscore, hyphen and forward slash (/) are allowed."
[5] "<font color=\"orange\">Other special characters or punctuations (if any) will be stripped off."
[6] "All data values are numeric."
[7] "A total of 744120 (14.4%) missing values were detected."
[8] "By default, missing values will be replaced by 1/5 of min positive values of their corresponding variables" [9] "Click the Proceed button if you accept the default practice;"
[10] "Or click the Missing Values button to use other methods."
mSet<-ReplaceMin(mSet); mSet<-PreparePrenormData(mSet) #Prepare data for normalization

Normalize

mSet<-Normalization(mSet, rowNorm="GroupPQN", transNorm="NULL", scaleNorm="NULL", ref="QC", ratio=FALSE, ratioNum=20) [1] 604 8540 mSet<-PlotNormSummary(mSet, "norm0", "png", 72, width=NA)

Fold change analysis

mSet <- FC.Anal(mSet, 2.0, 0) mSet <- PlotFC(mSet, "fc0", "png", 72, width=NA)`

[jessieolough]

Hi! Yes, it appears that MetaboAnalystR functions only provide images as outputs. This stackoverflow thread describes how you can plot images in the plot panel in RStudio.

One thing I have been doing is incorporating the images into a pdf output using RMarkdown. Below is a shortened example of how I have done this in a .Rmd file in RStudio, but here is also a link to a definitive guide to making pdf documents using RStudio.

---
title: "Metabolomics Report"
author: "jessieolough"
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)```

```{r Code-from-MetaboAnalyst, message=FALSE, warning=FALSE, include=FALSE}
library(MetaboAnalystR)
# Construct mSetObj
mSet<-InitDataObjects("pktable", "stat", FALSE)
# Read raw csv file
mSet<-Read.TextData(mSet, "annotations.csv", "colu", "disc");
# Check that the data is in the correct format for further analysis
mSet<-SanityCheckData(mSet)
# Replace zero/missing values with half of the smallest positive values in the original dataset
mSet<-ReplaceMin(mSet);
mSet<-SanityCheckData(mSet)
# Filter dataset (filter out 5% based on Interquantile range, IQR)
mSet<-FilterVariable(mSet, "none", -1, "F", 25, F)
# Normalise data
mSet<-PreparePrenormData(mSet)
mSet<-Normalization(mSet, "NULL", "LogNorm", "ParetoNorm", ratio=FALSE, ratioNum=20)
# Make a two-plot summary plot (exported as .png into directory)
mSet<-PlotNormSummary(mSet, "norm_0_", "png", 72, width=NA)```

```{r Insert-MetaboAnalyst-boxplots, echo=FALSE, fig.align="center", message=FALSE, warning=FALSE, out.width = "100%"}
library(rmarkdown)
library(knitr)
knitr::include_graphics("norm_0_dpi72.png")```