Commit d20b4048 authored by mirachirkova's avatar mirachirkova
Browse files

change results

parent f4bf0803
SEMG1
SEMG2
PIP
AQP2
MUC6
AQP2
PATE1
SERPINA5
PCA3
......@@ -27,4 +27,4 @@ STAC2
OR51E2
HPN
ACSM1
RPPH1
CLU
......@@ -67,7 +67,7 @@
"STAC2","-","-","-","+","-",1
"OR51E2","-","-","-","+","-",1
"ACSM1","-","-","-","+","-",1
"RPPH1","-","-","-","+","-",1
"CLU","-","-","-","+","-",1
"C2orf88","-","-","-","-","+",1
"APOBEC3C","-","-","-","-","+",1
"CA14","-","-","-","-","+",1
......
......@@ -2,4 +2,4 @@ DESeq 0.790475367665374
EBSeq 0.515586137502965
edgeR 0.522764214114926
voom 0.770472302946693
NOISeq 0.766533832527054
NOISeq 0.762570385003167
......@@ -37,19 +37,33 @@ voom_res <- readRDS(file = file.path(out, "voom_res.rds"))
noiseq_res <- readRDS(file = file.path(out, "NOISeq_res.rds"))
# Visualize results of differential expression
loginfo('Visualize results of differential expression')
pdf(file.path(out, "de_plots.pdf"))
#loginfo('Visualize results of differential expression')
h_results <- read.table(file=file.path(out, "hobotnica_scores.txt"), sep = " ", dec = ".")
colnames(h_results) <- c("names", "scores")
h_results <- h_results[order(h_results$scores, decreasing = TRUE), ]
colnames(cross_results) <- c("DESeq", "EBSeq", "edgeR", "NOISeq", "voom"
#pdf(file.path(out, "de_plots.pdf"))
library(gridExtra)
library(grid)
library(ggplot2)
library(lattice)
deseq2_v(deseq2_res, out)
#a <- ebseq_v(ebseq_res, out)
b <- edger_v(edger_res, out)
c <- voom_v(voom_res, out)
#d <- noiseq_v(noiseq_res, out)
grid.arrange(b, c, ncol=2, top = textGrob('EnhancedVolcano',
just = c('center'),
gp = gpar(fontsize = 32)))
dev.off()
deseq_plot <- deseq2_v(deseq2_res, out)
ebseq_plot <- ebseq_v(ebseq_res, out)
edger_plot <- edger_v(edger_res, out)
voom_plot <- voom_v(voom_res, out)
noiseq_plot <- noiseq_v(noiseq_res, out)
plots <- data.frame(deseq_plot, ebseq_plot, edger_plot,
voom_plot, noiseq_plot)
colnames(cross_results) <- c("DESeq", "EBSeq", "edgeR", "NOISeq", "voom", "count")
#grid.arrange(b, c, ncol=2, top = textGrob('EnhancedVolcano',
# just = c('center'),
# gp = gpar(fontsize = 32)))
#dev.off()
loginfo('Visualization results of differential expression is done')
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