RNA-seq

plot methods

running example

The script is in the "script" path, and the file used is in the "example_file" path

heatmap

Rscript heatmap.r KOVSWT.All.txt KOVSWT true pvalue 1 0.05 red blue white 0.01 10 45 7 7 2 T F 0

Vocano plot

Rscript volcano.R KOVSWT.All.txt 2 3 1 0.05 4 10 true Pvalue KOVSWT.Volcano.png KOVSWT.Volcano.txt KOVSWT.Volcano.pdf red blue grey 1.2 0.6 1 1.2 "#f0f0f0" 7 7

PCA

Rscript plot.r All.HTSeq.counts.txt KO1,KO2,KO3,KO4,WT1,WT2,WT3,WT4 KO,KO,KO,KO,WT,WT,WT,WT 6 8 RNA 6 6 2 9 0.8 1.5 1.0 1.2

GSEA

less KOVSWT.All.txt | cut -f1,2 | grep -i -w -v "NA" | sed '1d' | tr "a-z" "A-Z"  > GSEA.simple.rnk
top_num=20
software="GSEA/java/gsea2-2.2.2.jar"
gmt_dir="GSEA/all.v7.4/"

for gmt in $(ls ${gmt_dir} | grep ".gmt")
do
        name=$(echo ${gmt} | cut -d"." -f1-2 | less)
        java -cp $software  -Xmx4g xtools.gsea.GseaPreranked -gmx ${gmt_dir}"/"${gmt} \
     -collapse false -mode Max_probe -norm meandiv -nperm 1000 -rnk ./GSEA.simple.rnk -scoring_scheme weighted\
      -rpt_label ${name} -include_only_symbols true -make_sets true -plot_top_x ${top_num} -rnd_seed timestamp -set_max 500\
       -set_min 15 -zip_report false -out ./ -gui false
done

GO KEGG

get enrichment table

resultDir="./"
bash runGeneEnrichment.sh \
$resultDir \
geneEnrichment.r \
H_3VSC_3.log2FC1.Pvalue0.05.txt \
mm10_Annotation.xls \
H_3VSC_3 \
2 \
true \
geneName

example table:

GO_KEGG enrichment barplot

resultDir="./"
bash runBarPlotAll.sh \
$resultDir \
barplot.r \
H_3VSC_3.up_GO_BP.enrichment.xls,H_3VSC_3.all_GO_BP.enrichment.xls,H_3VSC_3.down_GO_BP.enrichment.xls,H_3VSC_3.down_Pathway.enrichment.xls,H_3VSC_3.up_Pathway.enrichment.xls,H_3VSC_3.all_Pathway.enrichment.xls \
H_3VSC_3,H_3VSC_3,H_3VSC_3,H_3VSC_3,H_3VSC_3,H_3VSC_3 \
enrichmentPlot.r \
8 \
7 \
20 \
40 \
60 \
Pvalue \
14 \
0.5 \
12 \
11 \
11 \
0.05 \
runBarPlot.sh