General Information
File: <%=x@filename%>
Type: FASTA
Sequence Length Range: <%=sl.range[1]%> to
<%=sl.range[2]%> bases
Total Sequences: <%=sum(x@seq.lengths)%>
Unique Sequences: <%=length(x@hash)%>
Nucleotide Frequency by Position
<%
basePlot(x)
ggsave(file.path(dir, 'images', 'basefreqs.png'), width=WIDTH, height=HEIGHT, dpi=DPI)
%>
Nucleotide Proportion by Position
<%
basePlot(x, type="proportion") + geom_hline(yintercept=0.25, color="purple")
ggsave(file.path(dir, 'images', 'baseprops.png'), width=WIDTH, height=HEIGHT, dpi=DPI)
%>
N Frequency by Position
<%
basePlot(x, bases='N')
ggsave(file.path(dir, 'images', 'nfreq.png'), width=WIDTH, height=HEIGHT, dpi=DPI)
%>
GC Content by Position
<%
gcPlot(x)
ggsave(file.path(dir, 'images', 'gc.png'), width=WIDTH, height=HEIGHT, dpi=DPI)
%>
Sequence Length Distribution
<%
seqlenPlot(x)
ggsave(file.path(dir, 'images', 'seqlengths.png'), width=WIDTH, height=HEIGHT, dpi=DPI)
%>
Most Frequent Sequences
<%
if (x@hashed) {
x <- makeHashTable(x)
print(x, type="html")
} else {
cat("No sequence frequency information available - readSeqFile() run with hash=FALSE")
}
%>
Report produced by the Bioconductor package qrqc
(c) Vince Buffalo 2011-2012, License: GPL 2.0