public class MotifDiscovererToolBox extends Object
MotifDiscoverer
.MotifDiscoverer
Constructor and Description |
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MotifDiscovererToolBox() |
Modifier and Type | Method and Description |
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static ImageResult |
plot(MotifDiscoverer motifDisc,
int component,
int motif,
Sequence sequence,
int startpos,
REnvironment r,
int width,
int height,
MotifDiscoverer.KindOfProfile kind)
This method creates a simple plot of the profile of scores for a sequence
and a start position.
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static ImageResult |
plotAndAnnotate(MotifDiscoverer motifDisc,
int component,
int motif,
Sequence sequence,
int startpos,
REnvironment r,
int width,
int height,
double yMin,
double yMax,
double threshold,
MotifDiscoverer.KindOfProfile kind)
This method creates a plot of the profile of scores for a sequence and a
start position and annotates bindings sites in the plot that have a higher
score than
threshold . |
public static ImageResult plot(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, MotifDiscoverer.KindOfProfile kind) throws Exception
motifDisc
- the MotifDiscoverer
component
- the index of the componentmotif
- the index of the motifsequence
- the given sequencestartpos
- the start position in the sequencer
- the R environment that is used for drawing the plotwidth
- the width of the image in pixelheight
- the height of the image in pixelkind
- the kind of the score profileImageResult
Exception
- if something went wrongpublic static ImageResult plotAndAnnotate(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, double yMin, double yMax, double threshold, MotifDiscoverer.KindOfProfile kind) throws Exception
threshold
.motifDisc
- the MotifDiscoverer
component
- the index of the componentmotif
- the index of the motifsequence
- the given sequencestartpos
- the start position in the sequencer
- the R environment that is used for drawing the plotwidth
- the width of the image in pixelheight
- the height of the image in pixelyMin
- the minimal value of the y-axisyMax
- the maximal value of the y-axisthreshold
- the threshold for the annotationkind
- the kind of the score profileException
- if some thing went wrong