From afa3bbee581681cd193531f2a490de82a8960403 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 4 Jan 2019 11:53:11 -0600
Subject: [PATCH] remove annotate peak vennpie and update test.
---
workflow/scripts/annotate_peaks.R | 22 +++++++++++++---------
workflow/tests/test_annotate_peaks.py | 6 ++----
2 files changed, 15 insertions(+), 13 deletions(-)
diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R
index 59bd269..98bb8bd 100644
--- a/workflow/scripts/annotate_peaks.R
+++ b/workflow/scripts/annotate_peaks.R
@@ -40,17 +40,26 @@ design <- read.csv(design_file, sep ='\t')
files <- as.list(as.character(design$Peaks))
names(files) <- design$Condition
+# Granges of files
+
+peaks <- lapply(files, readPeakFile, as = "GRanges", header = FALSE)
+peakAnnoList <- lapply(peaks, annotatePeak, TxDb=txdb, annoDb=annodb, tssRegion=c(-3000, 3000), verbose=FALSE)
+
+column_names <- c("chr", "start", "end", "width", "strand_1", "name", "score", "strand", "signalValue",
+ "pValue", "qValue", "peak", "annotation", "geneChr", "geneStart", "geneEnd",
+ "geneLength" ,"geneStrand", "geneId", "transcriptId", "distanceToTSS",
+ "ENSEMBL", "symbol", "geneName")
-peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb, annoDb=annodb, tssRegion=c(-3000, 3000), verbose=FALSE)
for(index in c(1:length(peakAnnoList))) {
- filename <- paste(names(files)[index],".chipseeker_annotation.csv",sep="")
- write.table(as.data.frame(peakAnnoList[[index]]),filename,sep=",",quote=F)
+ filename <- paste(names(peaks)[index], ".chipseeker_annotation.csv", sep="")
+ df <- as.data.frame(peakAnnoList[[index]])
+ colnames(df) <- column_names
+ write.table(df[ , !(names(df) %in% c('strand_1'))], filename, sep="," ,quote=F, row.names=F)
# Draw individual plots
# Define names of Plots
pie_name <- paste(names(files)[index],".chipseeker_pie.pdf",sep="")
- vennpie_name <- paste(names(files)[index],".chipseeker_vennpie.pdf",sep="")
upsetplot_name <- paste(names(files)[index],".chipseeker_upsetplot.pdf",sep="")
# Pie Plots
@@ -58,11 +67,6 @@ for(index in c(1:length(peakAnnoList))) {
plotAnnoPie(peakAnnoList[[index]])
dev.off()
- # Venn Diagrams
- pdf(vennpie_name)
- vennpie(peakAnnoList[[index]])
- dev.off()
-
# Upset Plot
pdf(upsetplot_name)
upsetplot(peakAnnoList[[index]])
diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py
index 077aa0e..a578da5 100644
--- a/workflow/tests/test_annotate_peaks.py
+++ b/workflow/tests/test_annotate_peaks.py
@@ -13,8 +13,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_annotate_peaks_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_pie.pdf'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_pie.pdf'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_pie.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf'))
annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.csv'
assert os.path.exists(annotation_file)
assert utils.count_lines(annotation_file) == 152839
@@ -23,8 +22,7 @@ def test_annotate_peaks_singleend():
@pytest.mark.pairedend
def test_annotate_peaks_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_pie.pdf'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_pie.pdf'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_pie.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_upsetplot.pdf'))
annotation_file = test_output_path + 'ENCSR217LRF.chipseeker_annotation.csv'
assert os.path.exists(annotation_file)
assert utils.count_lines(annotation_file) == 25390
--
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