This function plot different isomiRs proportion for each sample. It can show trimming events at both side, additions and nucleotides changes.
isoPlot(ids, type = "iso5", column = "condition")
ids | Object of class IsomirDataSeq. |
---|---|
type | String (iso5, iso3, add, subs, all) to indicate what isomiRs to use for the plot. See details for explanation. |
column | String indicating the column in
|
ggplot2::ggplot()
Object showing different isomiRs changes at
different positions.
There are four different values for type
parameter. To plot
trimming at 5' or 3' end, use type="iso5"
or type="iso3"
. Get a summary of all using type="all"
.
In this case, it will plot 3 positions at both side of the reference
position described at miRBase site. Each position refers to the number of
sequences that start/end before or after the miRBase reference. The
color indicates the sample group. The size of the point is proportional
to the number of total counts. The position at y
is the number of
different sequences.
Same logic applies to type="add"
and type="subs"
. However,
when type="add"
, the plot will refer to addition events from the
3' end of the reference position. Note that this additions don't match
to the precursor sequence, they are non-template additions.
In this case, only 3 positions after the 3' end
will appear in the plot. When type="subs"
, it will appear one
position for each nucleotide in the reference miRNA. Points
will indicate isomiRs with nucleotide changes at the given position.
When type="all"
a colar coordinate map will show
the abundance of each isomiR type in a single plot.
data(mirData) isoPlot(mirData, column="group")