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.

Revised WGCNA with GO-MWU analysis

WGCNA code

Stacked barplot with different colors for each bar

CHiP-Seq and ATAC-Seq

Creating plots mirrored along the y-axis

Good code example:

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:

Good code example:

Importing multiple files to R

Modified from this link.

coverageFiles <- list.files(pattern = "*bedgraph") #Create a file list for all 10 files to import
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:

Artificially grouping bars to create a grouped bar plot with an axis break:

My final code:

Updating R using updateR package