update the output dirs

_posts/0003-04-03-DE_Visualization_AdvancedR.md

@@ -33,7 +33,9 @@ Expression and differential expression files will be read into R. The R analysis
 Start RStudio, or launch a posit Cloud session, or if you are using AWS, navigate to the correct directory and then launch R:
 
 ```bash
-cd $RNA_HOME/de/ballgown/ref_only/
+mkdir $RNA_HOME/de/visualization_advanced
+cd $RNA_HOME/de/visualization_advanced
+
 R
 ```
 
@@ -46,16 +48,6 @@ library(gplots)
 library(GenomicRanges)
 library(ggrepel)
 
-#Set working directory where results files exist
-datadir = "~/workspace/rnaseq/de/ballgown/ref_only"
-outdir = "~/workspace/rnaseq/de/manual_viz"
-if (!dir.exists(outdir)) dir.create(outdir)
-
-setwd(datadir)
-
-# List the current contents of this directory
-dir()
-
 #Import expression results (TPM values) from the HISAT2/Stringtie pipeline (http://genomedata.org/rnaseq-tutorial/results/cshl2022/rnaseq/gene_tpm_all_samples.tsv)
 gene_expression = read.table("~/workspace/rnaseq/expression/stringtie/ref_only/gene_tpm_all_samples.tsv", header = TRUE, stringsAsFactors = FALSE, row.names = 1)
 
@@ -64,7 +56,6 @@ gene_names=read.table("~/workspace/rnaseq/de/htseq_counts/ENSG_ID2Name.txt", hea
 colnames(gene_names) = c("gene_id", "gene_name")
 
 #Import DE results from the HISAT2/htseq-count/DESeq2 pipeline (http://genomedata.org/cri-workshop/deseq2/DE_all_genes_DESeq2.tsv)
-setwd(outdir)
 results_genes = read.table("~/workspace/rnaseq/de/deseq2/DE_all_genes_DESeq2.tsv", sep = "\t", header = TRUE, stringsAsFactors = FALSE)
 
 ```