8.3 Activity: RStudio

8.3.1 Purpose

The purpose of this activity is to introduce the RStudio environment on SciServer for importing, exploring, filtering, and visualizing genomic data. Students will gain hands-on experience working with real bioinformatics output files (geNomad plasmid and virus summaries) and get a taste or foundational data analysis skills using R.

8.3.2 Learning Objectives

By the end of this activity, students will be able to:

1. Data import and environment setup
   • Load tabular data files into R/RStudio using functions such as read_tsv()
   • Navigate and use the RStudio interface, including file upload and script execution
2. Data exploration and manipulation
   • Explore datasets using basic R commands (e.g., viewing objects, inspecting column names)
   • Sort and filter data using base R and tidyverse functions (e.g., sort(), filter(), %>%)
   • Identify and subset biologically relevant data (e.g., contigs with AMR genes, non-provirus viral contigs)
3. Data visualization and reproducibility
   • Create and customize basic data visualizations using histogram plots in R (e.g., modifying titles and colors)
   • Write, annotate, and organize reproducible R scripts for data analysis workflows

8.3.3 Activity 1 – Import files to RStudio on SciServer

Estimated time: 10 min

8.3.3.1 Instructions

1. Download files.
   • Download two geNomad output files from Galaxy history below - plasmid summary and virus summary.
   • The files correspond to geNomad output for Zymo gut standard D6331 subset:
     • https://usegalaxy.org/u/valerie-g/h/genomad-plasmid-virus-summary-zymo-gut-standard-d6331-subset
2. Launch RStudio on SciServer.
   1. Log into https://sciserver.org.
   2. Navigate to SciServer ‘Compute’ (one of the cards on the bottom of the page).
   3. Click “Create container”.
   4. Give your container a name (eg. RStudio)
   5. In the “Compute Image” drop-down menu, select Bioconductor 3.17 (RStudio)
   6. Hit the green ‘Create’ button on the bottom.
   7. Click on the ‘RStudio’ Name to open RStudio window.
3. Upload files to RStudio on SciServer.
   1. Navigate to the Files pane located in the lower-right panel of the RStudio.
   2. Click the ‘Upload’ button in the toolbar of the Files pane.
   3. Click ‘Choose File’ to upload the two geNomad output files (you previously downloaded in Step 1 - uploading one at a time.
   4. You should now see two downloaded files in your ‘Files’ pane.

4. Load files into R/RStudio.
   1. Create a new file to store your R code by opening the File menu, selecting New File, and then R Script
   2. Enter the following two R commands into the new top left window of RStudio
      1. Load the R package called ‘tidyverse’ by entering the command library().
      2. Import a file of interest by using the function read_tsv().
         • See code block below to load the file “Galaxy1-[geNomad-plasmid-summary].tabular” and store it as a new object (variable) called e.g. ‘plasmids’.

      library(tidyverse)
      plasmids <- read_tsv("Galaxy1-[geNomad-plasmid-summary].tabular")

   3. Highlight both commands and then click ‘Run’.

8.3.3.2 Questions

1. Provide the command you used to import your geNomad-plasmid-summary file:

2. Provide command you used to import your geNomad-virus-summary file:

8.3.4 Activity 2 – Explore files in RStudio on SciServer

Estimated time: 10 min

8.3.4.1 Instructions

1. Use basic R commands to explore imported files in RStudio.
2. Craft your commands using an R Script - you will be asked to provide your R Script code.
   • Include all commands you used
   • Annotate all commands you used
   • See sample R Code below:

Your R Script for Activity 2 should include:

# Part 1: Plasmids

### Explore object
<your commands>
### Explore column names
<your commands>
### Sort file based on plasmid length, from high to low
<your commands>
### Filter file to only include contigs with detected AMRs (amr_genes)
<your commands>


# Part 2: Virus

### Explore object
<your commands>
### Explore column names
<your commands>
### Sort file based on virus length, from high to low
<your commands>
### Filter file to exclude Provirus
<your commands>

8.3.4.2 Questions

8.3.4.3 Part 1 - Explore geNomad plasmid summary file in RStudio

1. View your imported plasmid file by typing in the name of your object - plasmids.

   plasmids

Question: How many plasmid contigs (rows) are in your file?

2. View column names using function colnames().

   colnames(plasmids)

Question: Copy and paste column names below.

3. Sort plasmid contigs based on decreasing length, using function sort().
   • Store as a new object called “sorted”;
   • After sorting, to view the ‘sorted’ object, type ‘sorted’.
     • Note: the sort() command is a function from the base R package. It is available in R without installing any special libraries.
   • Your command will contain the following components:
     • sorted <- – assigns the result of the operation to a new variable
     • sort() – the function used to do the sorting
     • plasmid$length – points to the “length” column in the plasmids object
     • decreasing = TRUE – specifies that sorting should be descending rather than the default ascending.

Use these commands:

sorted <- sort( plasmids$length, decreasing = TRUE )
sorted

Question: What is the length of the largest contig length in a file? This should be the 1st number?

4. Filter plasmid contigs using the filter() function to retain only those that contain antimicrobial resistance (AMR) genes (amr_genes column); For this, you will need to remove the missing values (NA). Once filtered, view the filtered contigs by calling on the ‘filtered’ object.
   • Store as a new object called “filtered”;
   • After filtering, to view the ‘filtered’ object, type ‘filtered’.
     • Note: We use the dplyr filter() function and the %>% pipe operator in the example below, which are both part of the tidyverse ecosystem of package - a popular extension in R, and is not a base R function.
       • So, you can mix and match functions from different packages!
   • Your command includes the following operations:
     • %>% – is an operator that sends the output data from one command as the input data into the next command
     • filter() – this function selects rows based on a condition
     • != – is the “Not equal to” operator

Use these commands:

filtered <- plasmids %>% filter (amr_genes != "NA")
filtered

Question: How many plasmid contigs had an AMR gene?

8.3.4.4 Part 2 - Explore geNomad virus summary file in RStudio

• Use commands you learned in Part 1 above, as a guide to explore virus summary file.

1. View your imported virus file by typing in the name of your object.

1A: Type your command below.

1B: How many virus contigs (rows) are in your file?

2. View column names using function colnames().

2A: Type your command below.

2B: Copy and paste column names below.

3. Sort virus contigs based on decreasing length, using function sort(). Provide your commands and answer the question below.
   • Store as a new object called “sortedV”;
   • After sorting, to view the ‘sorted’ object, type ‘sortedV’.

3A: Type your commands below:
Command 1:
Command 2:

3B: What is the largest contig length in the file?

4. Filter viral contigs using filter() function to all viral contigs EXCEPT those identified as “Provirus” (topology column); For this, you will need to eliminate the “Provirus”.
   • Store as a new object called “filteredV”;
   • After filtering, to view the ‘filtered’ object, type ‘filteredV’.

4A: Type your commands below:
Command 1:
Command 2:

4B: How many viral contigs were NOT classified as Provirus?

8.3.5 Activity 3 – Plot and modify histogram of contig lengths

Estimated time: 10 min

8.3.5.1 Instructions

1. Use base R commands to plot and modify histogram in RStudio
2. Continue to add this code to your R Script.

8.3.5.2 Questions

8.3.5.3 Part 1 - Plot histogram of plasmid lengths

1. Plot histogram of plasmid contig lengths using function hist() and specifying the length column.
   • Your histogram will appear in the Plots tab (bottom right)

Use this command:

hist(plasmids$length)

1A: Paste resulting plot below.

2. Modify your histogram by changing the title to “Plasmid Length Distribution” Use this command:

   hist (plasmids$length, main = “Plasmid Length Distribution”)

2A: Paste resulting plot below.

3. Modify your histogram by changing histogram color to lightblue.

Use this command:

hist ( plasmids$length, main = "Plasmid Length Distribution", col = "lightblue" )

3A: Paste resulting plot below.

8.3.5.4 Part 2 - Plot histogram of virus lengths

1. Plot histogram of viral contig lengths using function hist() and specifying the length column
   • Your histogram will appear in the Plots tab (bottom right)

1A: Type your command below:

1B: Paste resulting plot below.

2. Modify your histogram by changing the title to “Virus Length Distribution”

2A: Type your command below:

2B: Paste resulting plot below.

3. Modify your histogram by changing histogram color to ‘lightgreen’.

3A: Type your command below:

3B: Paste resulting plot below.

8.3.5.5 Part 3 - Copy and paste your R Script below, which should be structured as follows:

# Import files into R Studio

### Plasmids
<your commands>
### Virus
<your commands>

# Explore imported files

### Plasmids
<your commands>
### Virus
<your commands>

# Plot histogram of lengths

### Plasmids
<your commands>
### Virus
<your commands>

Paste your R Script below.

8.3.6 Grading Criteria

• Download as Microsoft Word (.docx) and upload on Canvas

8.3.7 Footnotes

Resources

• Google Doc

Contributions and Affiliations

• Valeriya Gaysinskaya, Johns Hopkins University
• Frederick Tan, Johns Hopkins University

Last Revised: March 2026