Usage
plotAlignments(obj, ...)
"plotAlignments"(obj, ..., min.freq = 0, min.count = 1, top.n = 50, renumbered = obj$pars[["renumbered"]], add.other = TRUE)
"plotAlignments"(obj, ..., alns, ins.sites, highlight.pam = TRUE, show.plot = FALSE, target.loc = 17, pam.start = NA, pam.end = NA, ins.size = 2, legend.cols = 3, xlab = NULL, xtick.labs = NULL, xtick.breaks = NULL, plot.text.size = 2, axis.text.size = 8, legend.text.size = 6, highlight.guide = TRUE, guide.loc = NULL, tile.height = 0.55, max.insertion.size = 20, min.insertion.freq = 5, line.weight = 1, legend.symbol.size = ins.size, add.other = FALSE)
Arguments
obj
The object to be plotted
min.freq
i (
one sample (default: 0, i.e no frequency cutoff)
min.count
i (integer) only plot variants with count >= i in at least
one sample (default: 0, i.e no count cutoff)
top.n
(integer) Plot only the n most frequent variants
(default: 50)
renumbered
If TRUE, the x-axis is numbered with respect to the target
(default: TRUE)
add.other
Add a blank row labelled "Other" to the plot, for combining
with plotFreqHeatmap (default: TRUE (signature "CrisprSet") FALSE (signature "matrix"))
alns
A named character vector of aligned sequences, with insertions removed
ins.sites
A table of insertion_sites, which must include cols
named "start", "cigar" and "seq", for the start of the insertion in the
corresponding sequence
highlight.pam
should location of PAM with respect to the target site be
indicated by a box? (Default: TRUE) If TRUE, and pam.start and pam.end are not
supplied, PAM is inferred from target.loc
show.plot
Should the plot be displayed (TRUE) or just returned as
a ggplot object (FALSE). (Default: FALSE)
target.loc
The location of the zero point / cleavage location. Base n, where
the zero point is between bases n and n+1
pam.start
The first location of the PAM with respect to the reference.
pam.end
The last location of the PAM with respect to the reference.
Default is two bases after the pam.start
ins.size
The size of the symbols representing insertions within the plot.
legend.cols
The number of columns in the legend. (Default:3)
xlab
A title for the x-axis (Default: NULL)
xtick.labs
Labels for the x-axis ticks (Default: NULL)
xtick.breaks
Locations for x-axis tick breaks (Default: NULL)
plot.text.size
The size of the text inside the plot
axis.text.size
The size of the axis labels
legend.text.size
The size of the legend labels
highlight.guide
Should the guide be indicated by a box in
the reference sequence? (Default: TRUE)
guide.loc
The location of the guide region to be highlighted,
as an IRanges object. Will be inferred from target.loc if
highlight.guide = TRUE and no guide.loc is supplied, assuming the guide
plus PAM is 23bp (Default: NULL)
tile.height
The height of the tiles within the plot. (Default: 0.55)
max.insertion.size
The maximum length of an insertion to be shown in the
legend. If max.insertion.size = n, an insertion of length m > n will
be annotated as "mI" in the figure. (Default: 20)
min.insertion.freq
Display inserted sequences with frequency at least x
amongst the sequences with an insertion of this size and length (Default: 5)
line.weight
The line thickness for the vertical line indicating the
zero point (cleavage site) and the boxes for the guide and PAM. (Default: 1)
legend.symbol.size
The size of the symbols indicating insertions
in the legend. (Default: ins.size)