Commit 0726f957 authored by mirachirkova's avatar mirachirkova
Browse files

add new info to heatmaps

parent 517e902a
File added
output/DESeq_heatmap.png

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output/DESeq_heatmap.png

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output/DESeq_heatmap.png
output/DESeq_heatmap.png
output/DESeq_heatmap.png
output/DESeq_heatmap.png
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output/EBSeq_heatmap.png

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output/EBSeq_heatmap.png

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output/EBSeq_heatmap.png
output/EBSeq_heatmap.png
output/EBSeq_heatmap.png
output/EBSeq_heatmap.png
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output/NOISeq_heatmap.png

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output/NOISeq_heatmap.png

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output/NOISeq_heatmap.png
output/NOISeq_heatmap.png
output/NOISeq_heatmap.png
output/NOISeq_heatmap.png
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......@@ -20,11 +20,11 @@ AMACR
KRT13
SPINK2
PDK4
SEMA5B
TFF3
SEMA5B
STAC2
PTGS2
OR51E2
RPPH1
EMX2OS
HPN
ACSM1
RPPH1
......@@ -2,12 +2,12 @@
"SERPINA5","+","+","+","+","+",5
"CLDN2","+","+","+","+","-",4
"SPINK2","+","+","+","+","-",4
"EMX2OS","+","+","+","+","-",4
"AQP2","+","+","+","+","-",4
"PIP","+","+","+","+","-",4
"MFSD2A","+","-","+","+","-",3
"EMX2","+","+","+","-","-",3
"HOXB8","+","+","+","-","-",3
"EMX2OS","+","+","+","-","-",3
"TMEM114","+","+","+","-","-",3
"SEMG1","-","+","+","+","-",3
"PAEP","-","+","+","+","-",3
......@@ -66,6 +66,7 @@
"STAC2","-","-","-","+","-",1
"PTGS2","-","-","-","+","-",1
"OR51E2","-","-","-","+","-",1
"ACSM1","-","-","-","+","-",1
"RPPH1","-","-","-","+","-",1
"C2orf88","-","-","-","-","+",1
"APOBEC3C","-","-","-","-","+",1
......
......@@ -11,7 +11,7 @@
"SPINK2","-","+","+","+"
"KLHL14","-","-","-","-"
"MIR4508","-","-","-","-"
"EMX2OS","-","+","+","+"
"EMX2OS","-","-","+","+"
"NDRG4","-","-","-","-"
"SPINK13","-","-","-","-"
"RASL10B","-","-","-","-"
......
output/crossing_with_best.png

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output/crossing_with_best.png

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output/crossing_with_best.png
output/crossing_with_best.png
output/crossing_with_best.png
output/crossing_with_best.png
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output/edgeR_heatmap.png

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output/edgeR_heatmap.png

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output/edgeR_heatmap.png
output/edgeR_heatmap.png
output/edgeR_heatmap.png
output/edgeR_heatmap.png
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......@@ -2,4 +2,4 @@ DESeq 0.790475367665374
EBSeq 0.515586137502965
edgeR 0.522764214114926
voom 0.770472302946693
NOISeq 0.762927580399172
NOISeq 0.766985895218256
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output/voom_heatmap.png

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output/voom_heatmap.png

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output/voom_heatmap.png
output/voom_heatmap.png
output/voom_heatmap.png
output/voom_heatmap.png
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......@@ -97,12 +97,31 @@ if (save_flag == 1) {
# Visualize results of differential expression
loginfo('Visualize results of differential expression')
loginfo('Visualize results of differential expression into one pdf')
deseq_de <- deseq2_v(deseq2_res, out)
edger_de <- edger_v(edger_res, out)
voom_de <- voom_v(voom_res, out)
pdf(file.path(out, "de_plots.pdf"))
deseq2_v(deseq2_res, out)
deseq_de
ebseq_v(ebseq_res, out)
edger_v(edger_res, out)
voom_v(voom_res, out)
edger_de
voom_de
noiseq_v(noiseq_res, out)
dev.off()
loginfo('Vizualize results of differential expression into png')
png(file.path(out, "DESeq_de.png"))
deseq_de
dev.off()
png(file.path(out, "EBSeq_de.png"))
ebseq_v(ebseq_res, out)
dev.off()
png(file.path(out, "edgeR_de.png"))
edger_de
dev.off()
png(file.path(out, "voom_de.png"))
voom_de
dev.off()
png(file.path(out, "NOISeq_de.png"))
noiseq_v(noiseq_res, out)
dev.off()
loginfo('Visualization results of differential expression is done')
......@@ -162,7 +181,7 @@ dev.off()
png(file.path(out, "NOISeq_heatmap.png"))
noiseq_hm
dev.off()
loginfo('The end!')
loginfo('Heat map visualization is done')
loginfo('Calculate distance matrices for tools')
# Calculate dist matrices for tools
......
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