RNAseq_plots

A program for producing several graphs for RNAseq data, primarily with EdgeR and ggplot2

RNAseq_plots.R graphs dataframes of interest for RNAseq data mapped by Salmon. Note that a 'mapping' directory containing each sample's Salmon output directory (including the quant.sf file) is required. Included is the directory "RNAseq_plots_DemoData," which contains all needed files to test run this program and observe its outputs.

RNAseq_plots requires the following packages, which will be installed upon running:

• BiocManager (from bioconductor.org), which contains the following for differential expression analysis:
• tximport
• edgeR
  For output data plotting:
• ggplot2
• ggrepel
• tidyr

Syntax: RNAseq_plots.R <libraries.tsv> <-graph_option> <baseline_name & assessed_name>

RNAseq_plots.R requires 3 user arguments:

1. <libraries.tsv> must be a 2-column dataframe of library names and categories (tissue types, developmental stages, etc.) seperated by a tab. Don't include headers. A minimum of 3 replicates per category is required. Example dataframe from the demo data:

   MG_SK1    skin  
   MG_SK2    skin  
   MG_SK3    skin  
   MG_B1    barbel  
   MG_B2    barbel  
   MG_B3    barbel  
   

2. One RNAseq_plots.R graph option (given in <>):

• All graphs <-all>
• Read (CPM) Distribution <-CPMd>
• Multidimensional Scaling <-MDS>
• Biological Coefficient of Variation <-BCV>
• MA plot <-MA>
• Volcano plot of DGE <-Vol>