Assignment 2

HTML Compiled Notebook: A2_InikaPrasad-InikaPrasad.html

Objective: Time estimated: 5 hours Time taken XXX h

Progress Task 1: MA plot/volcano plot

Heat map + explanations

• Package ComplexHeatmap is not able to load, and so the heatmap doesn't have any colours.
• The error message is Error: package or namespace load failed for ‘ComplexHeatmap’: .onLoad failed in loadNamespace() for 'Cairo'
• Looking online, this seems to be a Mac OS graphics problem. May need to install XQuartz
• Xquartz starts a graphics device driver for the macOS system. It supports plotting both to the screen (the default) and to various graphics file formats. (Source: help file for Quartz)
• It must be installed manually since the Mac OS X ((Source: Download R for Mac *XQuartz installed and ComplexHeatMap package is now loaded
• I think my data has too many rows? I get a warning use_raster is automatically set to TRUE for a matrix with more than 2000 rows. You can control use_raster argument by explicitly setting TRUE/FALSE to it.`
• 'magick' package is suggested to install to give better rasterization.
• Downloaded the magick package and

Thresholded gene set enrichment

• download the gprofiler2 package: done

What annotation data?

Task 2: Managing references (1 hour estimated) Took 20 minutes. Save your references as a .txt file and you can convert it to a .bib file on the Mac itself.

Task 3: Uploading all data correctly (30-40 min estimated) The child node is giving me a lot of trouble. Knitting Assignment 1 into a trial document works just fine, and I am able to access objects from Assignment 1. However, when I try to do it in Assignment 2, I get the error message "Duplicate chunk label". Apparently, it's because plots will get overwritten if I have chunks that are named the same way (i.e. the default "unnamed chunk"). So I'm going through to label all my chunks in A1.

All chunks in A1 labelled, error persists. Also get the message

Error: The name of the input file cannot contain the special shell characters: [ <>()|\:&;#?*'] (attempted to copy to a version without those characters 'BCB420-Assignment-2.Rmd' however that file already exists) Execution halted

Trying to rename my file to not include any spaces. Error in file(con, "r" : cannot open the connection)

Looking at the files tab in R, it seems that A1_InikaPrasad/InikaPrasad has been renamed to A2_InikaPrasad:InikaPrasad. Changing the knit_child filename to this worked!

Trying after renaming and new session:

Conclusion & Outlook What I learned Next steps:

Footnotes & References Material adapted from