install.packages(“usethis”) #Install packages
usethis::use_course(“hglanz/rworkshop_Jan2021”) #Download materials from GitHub repo (https://github.com/hglanz/rworkshop_Jan2021) to machine
Category Archives: yaamini
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
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: 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