CG/CV transcriptomics

Helping Colleen with a comparative transcriptomics project for OSHV-infected and uninfected Pacific and eastern oysters to build skills and pipelines I’ll need for my RNASeq analysis later.

• Trimmed data
• Ran FastQC and MultiQC on untrimmed and trimmed samples
• Looked at FastQC and MultiQC reports for untrimmed and trimmed data. Most, if not all, of the trimmed samples failed the per base sequence content and sequence duplication levels sections.

Revised WGCNA with GO-MWU analysis

https://github.com/eimd-2019/project-EWD-transcriptomics/blob/master/analyses/WGCNA/WGCNA.md

WGCNA code

https://github.com/eimd-2019/project-EWD-transcriptomics/blob/master/analyses/WGCNA/WGCNA.Rmd

Stacked barplot with different colors for each bar

https://stackoverflow.com/questions/22781685/different-colors-for-each-bar-in-stacked-bar-graph-base-graphics

CHiP-Seq and ATAC-Seq

https://bioinformatics-core-shared-training.github.io/cruk-autumn-school-2017/ChIP/Materials/Lectures/Lecture4_Introduction%20to%20ChIP-seq%20and%20ATAC-seq_SS.pdf

Creating plots mirrored along the y-axis

Good code example: https://www.r-bloggers.com/making-back-to-back-histograms/

Adding lines to barplots + 2 y-axes

Explanation as to why base plot should be saved as a separate object and referenced in subsequent plots: https://www.r-bloggers.com/adding-lines-or-points-to-an-existing-barplot/

Good code example: https://stackoverflow.com/questions/15277712/adding-lines-to-barplot-in-a-different-y-axis-in-r

Importing multiple files to R

Modified from this link.

coverageFiles <- list.files(pattern = "*bedgraph") #Create a file list for all 10 files to import
list2env(lapply(setNames(coverageFiles,
make.names(gsub("s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_", "", coverageFiles))), read.table),
envir = .GlobalEnv) #Import files with list2env. Use lapply to setNames of the files by taking all the common parts of their names out. Files will be named zr2096_#_5x.bedgraph

Creating a plot with a gapped axis

I used the plotrix package to add an axis break to a grouped bar plot.

R Studio notes: https://rstudio-pubs-static.s3.amazonaws.com/235467_5abd31ab564a43c9ae0f18cdd07eebe7.html

Artificially grouping bars to create a grouped bar plot with an axis break: https://stackoverflow.com/questions/24202245/grouped-barplot-with-cut-y-axis

My final code: https://github.com/eimd-2019/NIX-project/blob/master/scripts/Population-versus-Year%20Graph.R

Updating R using updateR package

https://www.linkedin.com/pulse/3-methods-update-r-rstudio-windows-mac-woratana-ngarmtrakulchol