settings: Setting display parameters to control the look and feel of...
In ivanek/Gviz: Plotting data and annotation information along genomic coordinates
settings R Documentation
Setting display parameters to control the look and feel of the plots
Description
The genome track plots in this package are all highly customizable by means
of so called 'display parameters'. This page highlights the use of these
parameters and list all available settings for the different track classes.
Arguments
scheme
A named nested list of display parameters, where the first
level of nesting represents Gviz track object classes, and the second level
of nesting represents parameters.
name
A character scalar with the scheme name.
Details
All of the package's track objects inherit the dp slot from the
GdObject parent class, which is the main container to
store an object's display parameters. Internally, the content of this slot
has to be an object of class DisplayPars, but the user
is usually not exposed to this low level implementation. Instead, there are
two main interaction points, namely the individual object constructor
functions and the final plotTracks function. In both cases,
all additional arguments that are not caught by any of the formally defined
function parameters are being interpreted as additional display parameters
and are automatically added to the aforementioned slot. The main difference
here is that display parameters that are passed on to the constructor
function are specific for an individual track object, whereas those supplied
to the plotTracks function will be applied to all the objects in the
plotting list. Not all display parameters have an effect on the plotting of
all track classes, and those will be silently ignored.
One can query the available display parameters for a given class as well as
their default values by calling the availableDisplayPars
function, or by inspecting the man pages of the individual track classes.
The structure of the classes defined in this package is hierarchical, and so
are the available display parameters, i.e., all objects inherit the
parameters defined in the commom GdObject parent class, and so on.
Once a track object has been created, the display parameters are still open
for modification. To this end, the DisplayPars replacement
method is available for all objects inheriting from class GdObject.
The method takes a named list of parameters as input, e.g.:
displayPars(foo) <- list(col="red", lwd=2)
In the same spirit, the currently set display parameters for the object
foo can be inferred using the displayPars method directly,
e.g.:
displayPars(foo)
For track objects inheriting from class
AnnotationTrack, display parameters that are not
formally defined in the class definition or in any of the parent classes are
considered to be valid R color identifiers that are used to distinguish
between different types of annotation features. For instance, the parameter
'miRNA' will be used to color all annotation features of class miRNA. The
annotation types can be set in the constructor function of the track object
via the feature argument. For most of the tracks that have been
inferred from one of the online repositories, this classification will
usually be downloaded along with the actual annotation data.
Users might find themselves changing the same parameters over and over
again, and it would make sense to register these modifications in a central
location once and for all. To this end the Gviz package supports display
parameter schemes. A scheme is essentially just a bunch of nested named
lists, where the names on the first level of nesting should correspond to
track class names, and the names on the second level to the display
parameters to set. The currently active schmeme can be changed by setting
the global option Gviz.scheme, and a new scheme can be registered by
using the addScheme function, providing both the list and the name
for the new scheme. The getScheme function is useful to get the
current scheme as a list structure, for instance to use as a skeleton for
your own custom scheme.
In order to make these settings persitant across R sessions one can create
one or several schemes in the global environment in the special object
.GvizSchemes, for instance by putting the necessary code in the
.Rprofile file. This object needs to be a named list of schemes, and
it will be collected when the Givz package loads. Its content is then
automatically added to the collection of available schemes.
Please note that because display parameters are stored with the track
objects, a scheme change only has an effect on those objects that are
created after the change has taken place.
Value
The getScheme function returns current scheme as a list structure.
Display Parameters
- GenomeAxisTrack:
-
add35=FALSE: Logical scalar. Add 3' to 5' direction
indicators.
add53=FALSE: Logical scalar. Add 5' to 3' direction
indicators.
background.title="transparent": Character scalar. The
background color for the title panel. Defaults to omit the background.
cex.id=0.7: Numeric scalar. The text size for the optional
range annotation.
cex=0.8: Numeric scalar. The overall font expansion factor
for the axis annotation text.
col.border.title="transparent": Integer or character scalar.
The border color for the title panels.
lwd.border.title=1: Integer scalar. The border width for the
title panels.
col.id="white": Character scalar. The text color for the
optional range annotation.
col.range="cornsilk4": Character scalar. The border color for
highlighted regions on the axis.
distFromAxis=1: Numeric scalar. Control the distance of the
axis annotation from the tick marks.
exponent=NULL: Numeric scalar. The exponent for the axis
coordinates, e.g., 3 means mb, 6 means gb, etc. The default is to
automatically determine the optimal exponent.
fill.range="cornsilk3": Character scalar. The fill color for
highlighted regions on the axis.
fontcolor="#808080": Character scalar. The font color for the
axis annotation text.
fontsize=10: Numeric scalar. Font size for the axis
annotation text in points.
labelPos="alternating": Character vector, one in
"alternating", "revAlternating", "above" or "below". The vertical
positioning of the axis labels. If scale is not NULL, the
possible values are "above", "below" and "beside".
littleTicks=FALSE: Logical scalar. Add more fine-grained tick
marks.
lwd=2: Numeric scalar. The line width for the axis
elementes.
scale=NULL: Numeric scalar. If not NULL a small scale
is drawn instead of the full axis, if the value is between 0 and 1 it is
interpreted as a fraction of the current plotting region, otherwise as an
absolute length value in genomic coordinates.
showId=FALSE: Logical scalar. Show the optional range
highlighting annotation.
showTitle=FALSE: Logical scalar. Plot a title panel. Defaults
to omit the title panel.
ticksAt=NULL: Numeric scalar. The exact x-position for
tickmarks (in base-pairs).
size=NULL: Numeric scalar. The relative size of the track.
Can be overridden in the plotTracks function. Defaults to the
ideal size based on the other track settings.
col="darkgray": Character scalar. The color for the axis
lines and tickmarks.
Inherited from class GdObject:
alpha=1: Numeric scalar. The transparency for all track
items.
alpha.title=NULL: Numeric scalar. The transparency for the
title panel.
background.panel="transparent": Integer or character scalar.
The background color of the content panel.
background.legend="transparent": Integer or character scalar.
The background color for the legend.
cex.axis=NULL: Numeric scalar. The expansion factor for the
axis annotation. Defaults to NULL, in which case it is automatically
determined based on the available space.
cex.title=NULL: Numeric scalar. The expansion factor for the
title panel. This effects the fontsize of both the title and the axis, if
any. Defaults to NULL, which means that the text size is
automatically adjusted to the available space.
col.axis="white": Integer or character scalar. The font and
line color for the y axis, if any.
col.frame="lightgray": Integer or character scalar. The line
color used for the panel frame, if frame==TRUE
col.grid="#808080": Integer or character scalar. Default
line color for grid lines, both when type=="g" in
DataTracks and when display parameter grid==TRUE.
col.line=NULL: Integer or character scalar. Default colors
for plot lines. Usually the same as the global col parameter.
col.symbol=NULL: Integer or character scalar. Default colors
for plot symbols. Usually the same as the global col parameter.
col.title="white": Integer or character scalar. The border
color for the title panels
collapse=TRUE: Boolean controlling whether to collapse the
content of the track to accomodate the minimum current device resolution.
See collapsing for details.
fill="lightgray": Integer or character scalar. Default fill
color setting for all plotting elements, unless there is a more specific
control defined elsewhere.
fontface.title=2: Integer or character scalar. The font face
for the title panels.
fontface=1: Integer or character scalar. The font face for
all text, unless a more specific definition exists.
fontfamily.title="sans": Integer or character scalar. The
font family for the title panels.
fontfamily="sans": Integer or character scalar. The font
family for all text, unless a more specific definition exists.
frame=FALSE: Boolean. Draw a frame around the track when
plotting.
grid=FALSE: Boolean, switching on/off the plotting of a
grid.
h=-1: Integer scalar. Parameter controlling the number of
horizontal grid lines, see panel.grid for details.
lineheight=1: Numeric scalar. The font line height for all
text, unless a more specific definition exists.
lty.grid="solid": Integer or character scalar. Default line
type for grid lines, both when type=="g" in DataTracks
and when display parameter grid==TRUE.
lty="solid": Numeric scalar. Default line type setting for
all plotting elements, unless there is a more specific control defined
elsewhere.
lwd.title=1: Integer scalar. The border width for the title
panels
lwd.grid=1: Numeric scalar. Default line width for grid
lines, both when type=="g" in DataTracks and when
display parameter grid==TRUE.
min.distance=1: Numeric scalar. The minimum pixel distance
before collapsing range items, only if collapse==TRUE. See
collapsing for details.
min.height=3: Numeric scalar. The minimum range height in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
min.width=1: Numeric scalar. The minimum range width in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
reverseStrand=FALSE: Logical scalar. Set up the plotting
coordinates in 3' -> 5' direction if TRUE. This will effectively
mirror the plot on the vertical axis.
rotation.title=90: The rotation angle for the text in the
title panel. Even though this can be adjusted, the automatic resizing of the
title panel will currently not work, so use at own risk.
rotation=0: The rotation angle for all text unless a more
specific definiton exists.
showAxis=TRUE: Boolean controlling whether to plot a y axis
(only applies to track types where axes are implemented).
v=-1: Integer scalar. Parameter controlling the number of
vertical grid lines, see panel.grid for details.
- DataTrack:
-
aggregateGroups=FALSE: Logical scalar. Aggregate the values
within a sample group using the aggregation funnction specified in the
aggregation parameter.
aggregation="mean": Function or character scalar. Used to
aggregate values in windows or for collapsing overlapping items. The
function has to accept a numeric vector as a single input parameter and has
to return a numeric scalar with the aggregated value. Alternatively, one of
the predefined options mean, median sum, min,
max or extreme can be supplied as a character scalar. Defaults
to mean.
missingAsZero=TRUE: Logical scalar. Defines how the missing
values are treated in the aggregation procedure with running window. Setting
it to TRUE fills empty positions with zeros, which is default.
FALSE fills empty positions with NA.
alpha.confint=0.3: Numeric scalar. The transparency for the
confidence intervalls in confint-type plots.
amount=NULL: Numeric scalar. Amount of jittering in xy-type
plots. See panel.xyplot for details.
baseline=NULL: Numeric scalar. Y-axis position of an optional
baseline. This parameter has a special meaning for mountain-type and
polygon-type plots, see the 'Details' section in
DataTrack for more information.
box.legend=FALSE: Logical scalar. Draw a box around a
legend.
box.ratio=1: Numeric scalar. Parameter controlling the
boxplot appearance. See panel.bwplot for details.
box.width=NULL: Numeric scalar. Parameter controlling the
boxplot appearance. See panel.bwplot for details.
grid=FALSE: Logical vector. Draw a line grid under the track
content.
cex.legend=0.8: Numeric scalar. The size factor for the
legend text.
cex.sampleNames=NULL: Numeric scalar. The size factor for the
sample names text in heatmap or horizon plots. Defaults to an automatic
setting.
cex=0.7: Numeric scalar. The default pixel size for plotting
symbols.
coef=1.5: Numeric scalar. Parameter controlling the boxplot
appearance. See panel.bwplot for details.
col.baseline=NULL: Character scalar. Color for the optional
baseline, defaults to the setting of col.
col.confint=NA: Character vector. Border colors for the
confidence intervals for confint-type plots.
col.boxplotFrame="#808080": Character scalar. Line color of
the frame around grouped boxplots.
col.histogram="#808080": Character scalar. Line color in
histogram-type plots.
col.horizon=NA: The line color for the segments in the
horizon-type plot. See horizonplot for details.
col.mountain=NULL: Character scalar. Line color in
mountain-type and polygon-type plots, defaults to the setting of
col.
col.sampleNames="white": Character or integer scalar. The
color used for the sample names in heatmap plots.
col=c("#0080ff", "#ff00ff", "darkgreen", "#ff0000", "orange",
"#00ff00", "brown"): Character or integer vector. The color used for all
line and symbol elements, unless there is a more specific control defined
elsewhere. Unless groups are specified, only the first color in the
vector is usually regarded.
collapse=FALSE: Logical scalar. Collapse overlapping ranges
and aggregate the underlying data.
degree=1: Numeric scalar. Parameter controlling the loess
calculation for smooth and mountain-type plots. See
panel.loess for details.
do.out=TRUE: Logical scalar. Parameter controlling the
boxplot appearance. See panel.bwplot for details.
evaluation=50: Numeric scalar. Parameter controlling the
loess calculation for smooth and mountain-type plots. See
panel.loess for details.
factor=0.5: Numeric scalar. Factor to control amount of
jittering in xy-type plots. See panel.xyplot for details.
family="symmetric": Character scalar. Parameter controlling
the loess calculation for smooth and mountain-type plots. See
panel.loess for details.
fill.confint=NULL: Character vector. Fill colors for the
confidence intervals for confint-type plots.
fill.histogram=NULL: Character scalar. Fill color in
histogram-type plots, defaults to the setting of fill.
fill.horizon=c("#B41414", "#E03231", "#F7A99C", "#9FC8DC",
"#468CC8", "#0165B3"): The fill colors for the segments in the
horizon-type plot. This should be a vector of length six, where the
first three entries are the colors for positive changes, and the latter
three entries are the colors for negative changes. Defaults to a red-blue
color scheme. See horizonplot for details.
fill.mountain=c("#CCFFFF", "#FFCCFF"): Character vector of
length 2. Fill color in mountain-type and polygon-type plots.
fontface.legend=NULL: Integer or character scalar. The font
face for the legend text.
fontfamily.legend=NULL: Integer or character scalar. The font
family for the legend text.
fontsize.legend=NULL: Numeric scalar. The pixel size for the
legend text.
fontcolor.legend="#808080": Integer or character scalar. The
font color for the legend text.
gradient=c("#F7FBFF", "#DEEBF7", "#C6DBEF", "#9ECAE1",
"#6BAED6", "#4292C6", "#2171B5", "#08519C", "#08306B"): Character vector.
The base colors for the gradient plotting type or the heatmap
type with a single group. When plotting heatmaps with more than one group,
the col parameter can be used to control the group color scheme,
however the gradient will always be from white to 'col' and thus does not
offer as much flexibility as this gradient parameter.
groups=NULL: Vector coercable to a factor. Optional sample
grouping. See 'Details' section in DataTrack for
further information.
horizon.origin=0: The baseline relative to which changes are
indicated on the horizon-type plot. See horizonplot for
details.
horizon.scale=NULL: The scale for each of the segments in the
horizon-type plot. Defaults to 1/3 of the absolute data range. See
horizonplot for details.
jitter.x=FALSE: Logical scalar. Toggle on jittering on the x
axis in xy-type plots. See panel.xyplot for details.
jitter.y=FALSE: Logical scalar. Toggle off jittering on the y
axis in xy-type plots. See panel.xyplot for details.
levels.fos=NULL: Numeric scalar. Parameter controlling the
boxplot appearance. See panel.bwplot for details.
legend=TRUE: Boolean triggering the addition of a legend to
the track to indicate groups. This only has an effect if at least two groups
are present.
lineheight.legend=NULL: Numeric scalar. The line height for
the legend text.
lty.baseline=NULL: Character or numeric scalar. Line type of
the optional baseline, defaults to the setting of lty.
lty.mountain=NULL: Character or numeric scalar. Line type in
mountain-type and polygon-type plots, defaults to the setting of
lty.
lwd.baseline=NULL: Numeric scalar. Line width of the optional
baseline, defaults to the setting of lwd.
lwd.mountain=NULL: Numeric scalar. Line width in
mountain-type and polygon-type plots, defaults to the setting of
lwd.
min.distance=0: Numeric scalar. The mimimum distance in pixel
below which to collapse ranges.
na.rm=FALSE: Boolean controlling whether to discard all NA
values when plotting or to keep empty spaces for NAs
ncolor=100: Integer scalar. The number of colors for the
'gradient' plotting type
notch.frac=0.5: Numeric scalar. Parameter controlling the
boxplot appearance. See panel.bwplot for details.
notch=FALSE: Logical scalar. Parameter controlling the
boxplot appearance. See panel.bwplot for details.
pch=20: Integer scalar. The type of glyph used for plotting
symbols.
separator=0: Numeric scalar. Number of pixels used to
separate individual samples in heatmap- and horizon-type plots.
showColorBar=TRUE: Boolean. Indicate the data range color
mapping in the axis for 'heatmap' or 'gradient' types.
showSampleNames=FALSE: Boolean. Display the names of the
individual samples in a heatmap or a horizon plot.
size=NULL: Numeric scalar. The relative size of the track.
Can be overridden in the plotTracks function. By default the
size will be set automatically based on the selected plotting type.
span=0.2: Numeric scalar. Parameter controlling the loess
calculation for smooth and mountain-type plots. See
panel.loess for details.
stackedBars=TRUE: Logical scalar. When there are several data
groups, draw the histogram-type plots as stacked barplots or grouped side by
side.
stats=X[[i]]: Function. Parameter controlling the boxplot
appearance. See panel.bwplot for details.
transformation=NULL: Function. Applied to the data matrix
prior to plotting or when calling the score method. The function
should accept exactly one input argument and its return value needs to be a
numeric vector which can be coerced back into a data matrix of identical
dimensionality as the input data.
type="p": Character vector. The plot type, one or several in
p,l, b, a, a_confint, s, g,
r, S, confint, smooth, histogram,
mountain, polygon, h, boxplot, gradient,
heatmap, horizon. See 'Details' section in
DataTrack for more information on the individual
plotting types.
varwidth=FALSE: Logical scalar. Parameter controlling the
boxplot appearance. See panel.bwplot for details.
window=NULL: Numeric or character scalar. Aggregate the rows
values of the data matrix to window equally sized slices on the data
range using the method defined in aggregation. If negative, apply a
running window of size windowSize using the same aggregation method.
Alternatively, the special value auto causes the function to
determine the optimal window size to avoid overplotting, and fixed
uses fixed-size windows of size windowSize.
windowSize=NULL: Numeric scalar. The size of the running
window when the value of window is negative.
ylim=NULL: Numeric vector of length 2. The range of the
y-axis scale.
yTicksAt=NULL: Numeric vector. The points at which y-axis
tick-marks are to be drawn. By default, when NULL, tickmark locations
are computed.
Inherited from class GdObject:
alpha=1: Numeric scalar. The transparency for all track
items.
alpha.title=NULL: Numeric scalar. The transparency for the
title panel.
background.panel="transparent": Integer or character scalar.
The background color of the content panel.
background.title="lightgray": Integer or character scalar.
The background color for the title panel.
background.legend="transparent": Integer or character scalar.
The background color for the legend.
cex.axis=NULL: Numeric scalar. The expansion factor for the
axis annotation. Defaults to NULL, in which case it is automatically
determined based on the available space.
cex.title=NULL: Numeric scalar. The expansion factor for the
title panel. This effects the fontsize of both the title and the axis, if
any. Defaults to NULL, which means that the text size is
automatically adjusted to the available space.
col.axis="white": Integer or character scalar. The font and
line color for the y axis, if any.
col.border.title="white": Integer or character scalar. The
border color for the title panels.
col.frame="lightgray": Integer or character scalar. The line
color used for the panel frame, if frame==TRUE
col.grid="#808080": Integer or character scalar. Default
line color for grid lines, both when type=="g" in
DataTracks and when display parameter grid==TRUE.
col.line=NULL: Integer or character scalar. Default colors
for plot lines. Usually the same as the global col parameter.
col.symbol=NULL: Integer or character scalar. Default colors
for plot symbols. Usually the same as the global col parameter.
col.title="white": Integer or character scalar. The border
color for the title panels
fill="lightgray": Integer or character scalar. Default fill
color setting for all plotting elements, unless there is a more specific
control defined elsewhere.
fontcolor="black": Integer or character scalar. The font
color for all text, unless a more specific definition exists.
fontface.title=2: Integer or character scalar. The font face
for the title panels.
fontface=1: Integer or character scalar. The font face for
all text, unless a more specific definition exists.
fontfamily.title="sans": Integer or character scalar. The
font family for the title panels.
fontfamily="sans": Integer or character scalar. The font
family for all text, unless a more specific definition exists.
fontsize=12: Numeric scalar. The font size for all text,
unless a more specific definition exists.
frame=FALSE: Boolean. Draw a frame around the track when
plotting.
h=-1: Integer scalar. Parameter controlling the number of
horizontal grid lines, see panel.grid for details.
lineheight=1: Numeric scalar. The font line height for all
text, unless a more specific definition exists.
lty.grid="solid": Integer or character scalar. Default line
type for grid lines, both when type=="g" in DataTracks
and when display parameter grid==TRUE.
lty="solid": Numeric scalar. Default line type setting for
all plotting elements, unless there is a more specific control defined
elsewhere.
lwd.border.title=1: Integer scalar. The border width for the
title panels.
lwd.title=1: Integer scalar. The border width for the title
panels
lwd.grid=1: Numeric scalar. Default line width for grid
lines, both when type=="g" in DataTracks and when
display parameter grid==TRUE.
lwd=1: Numeric scalar. Default line width setting for all
plotting elements, unless there is a more specific control defined
elsewhere.
min.height=3: Numeric scalar. The minimum range height in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
min.width=1: Numeric scalar. The minimum range width in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
reverseStrand=FALSE: Logical scalar. Set up the plotting
coordinates in 3' -> 5' direction if TRUE. This will effectively
mirror the plot on the vertical axis.
rotation.title=90: The rotation angle for the text in the
title panel. Even though this can be adjusted, the automatic resizing of the
title panel will currently not work, so use at own risk.
rotation=0: The rotation angle for all text unless a more
specific definiton exists.
showAxis=TRUE: Boolean controlling whether to plot a y axis
(only applies to track types where axes are implemented).
showTitle=TRUE: Boolean controlling whether to plot a title
panel. Although this can be set individually for each track, in multi-track
plots as created by plotTracks there will still be an empty
placeholder in case any of the other tracks include a title. The same holds
true for axes. Note that the the title panel background color could be set
to transparent in order to completely hide it.
v=-1: Integer scalar. Parameter controlling the number of
vertical grid lines, see panel.grid for details.
- IdeogramTrack:
-
background.title="transparent": Character scalar. The
background color for the title panel. Defaults to omit the background.
bevel=0.45: Numeric scalar, between 0 and 1. The level of
smoothness for the two ends of the ideogram.
centromereShape="triangle": Character scalar. The shape of
the centromere. Only "triangle" or "circle" is accepted. Default to
"triangle"
cex.bands=0.7: Numeric scalar. The font expansion factor for
the chromosome band identifier text.
cex=0.8: Numeric scalar. The overall font expansion factor
for the chromosome name text.
col="red": Character scalar. The border color used for the
highlighting of the currently displayed genomic region.
col.border.title="transparent": Integer or character scalar.
The border color for the title panels.
lwd.border.title=1: Integer scalar. The border width for the
title panels.
fill="#FFE3E6": Character scalar. The fill color used for the
highlighting of the currently displayed genomic region.
fontface=1: Character scalar. The font face for the
chromosome name text.
fontfamily="sans": Character scalar. The font family for the
chromosome name text.
fontcolor="#808080": Character scalar. The font color for the
chromosome name text.
fontsize=10: Numeric scalar. The font size for the chromosome
name text.
outline=FALSE: Logical scalar. Add borders to the individual
chromosome staining bands.
showBandId=FALSE: Logical scalar. Show the identifier for the
chromosome bands if there is space for it.
lty=1: Character or integer scalar. The line type used for
the highlighting of the currently displayed genomic region.
lwd=1: Numeric scalar. The line width used for the
highlighting of the currently displayed genomic region.
showId=TRUE: Logical scalar. Indicate the chromosome name
next to the ideogram.
showTitle=FALSE: Logical scalar. Plot a title panel. Defaults
to omit the title panel.
size=NULL: Numeric scalar. The relative size of the track.
Defaults to automatic size setting. Can also be overridden in the
plotTracks function.
Inherited from class GdObject:
alpha=1: Numeric scalar. The transparency for all track
items.
alpha.title=NULL: Numeric scalar. The transparency for the
title panel.
background.panel="transparent": Integer or character scalar.
The background color of the content panel.
background.legend="transparent": Integer or character scalar.
The background color for the legend.
cex.axis=NULL: Numeric scalar. The expansion factor for the
axis annotation. Defaults to NULL, in which case it is automatically
determined based on the available space.
cex.title=NULL: Numeric scalar. The expansion factor for the
title panel. This effects the fontsize of both the title and the axis, if
any. Defaults to NULL, which means that the text size is
automatically adjusted to the available space.
col.axis="white": Integer or character scalar. The font and
line color for the y axis, if any.
col.frame="lightgray": Integer or character scalar. The line
color used for the panel frame, if frame==TRUE
col.grid="#808080": Integer or character scalar. Default
line color for grid lines, both when type=="g" in
DataTracks and when display parameter grid==TRUE.
col.line=NULL: Integer or character scalar. Default colors
for plot lines. Usually the same as the global col parameter.
col.symbol=NULL: Integer or character scalar. Default colors
for plot symbols. Usually the same as the global col parameter.
col.title="white": Integer or character scalar. The border
color for the title panels
collapse=TRUE: Boolean controlling whether to collapse the
content of the track to accomodate the minimum current device resolution.
See collapsing for details.
fontface.title=2: Integer or character scalar. The font face
for the title panels.
fontfamily.title="sans": Integer or character scalar. The
font family for the title panels.
frame=FALSE: Boolean. Draw a frame around the track when
plotting.
grid=FALSE: Boolean, switching on/off the plotting of a
grid.
h=-1: Integer scalar. Parameter controlling the number of
horizontal grid lines, see panel.grid for details.
lineheight=1: Numeric scalar. The font line height for all
text, unless a more specific definition exists.
lty.grid="solid": Integer or character scalar. Default line
type for grid lines, both when type=="g" in DataTracks
and when display parameter grid==TRUE.
lwd.title=1: Integer scalar. The border width for the title
panels
lwd.grid=1: Numeric scalar. Default line width for grid
lines, both when type=="g" in DataTracks and when
display parameter grid==TRUE.
min.distance=1: Numeric scalar. The minimum pixel distance
before collapsing range items, only if collapse==TRUE. See
collapsing for details.
min.height=3: Numeric scalar. The minimum range height in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
min.width=1: Numeric scalar. The minimum range width in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
reverseStrand=FALSE: Logical scalar. Set up the plotting
coordinates in 3' -> 5' direction if TRUE. This will effectively
mirror the plot on the vertical axis.
rotation.title=90: The rotation angle for the text in the
title panel. Even though this can be adjusted, the automatic resizing of the
title panel will currently not work, so use at own risk.
rotation=0: The rotation angle for all text unless a more
specific definiton exists.
showAxis=TRUE: Boolean controlling whether to plot a y axis
(only applies to track types where axes are implemented).
v=-1: Integer scalar. Parameter controlling the number of
vertical grid lines, see panel.grid for details.
- AnnotationTrack:
-
arrowHeadWidth=30: Numeric scalar. The width of the arrow
head in pixels if shape is fixedArrow.
arrowHeadMaxWidth=40: Numeric scalar. The maximum width of
the arrow head in pixels if shape is arrow.
cex.group=0.6: Numeric scalar. The font expansion factor for
the group-level annotation.
cex=1: Numeric scalar. The font expansion factor for item
identifiers.
col.line="darkgray": Character scalar. The color used for
connecting lines between grouped items. Defaults to a light gray, but if set
to NULL the same color as for the first item in the group is used.
col="transparent": Character or integer scalar. The border
color for all track items.
featureAnnotation=NULL: Character scalar. Add annotation
information to the individual track elements. This can be a value in
id, group or feature. Defaults to id. Only
works if showFeatureId is not FALSE.
fill="lightblue": Character or integer scalar. The fill
color for untyped items. This is also used to connect grouped items. See
grouping for details.
fontfamily.group="sans": Character scalar. The font family
for the group-level annotation.
fontcolor.group="#808080": Character or integer scalar. The
font color for the group-level annotation.
fontcolor.item="white": Character or integer scalar. The font
color for item identifiers.
fontface.group=2: Numeric scalar. The font face for the
group-level annotation.
fontsize.group=12: Numeric scalar. The font size for the
group-level annotation.
groupAnnotation=NULL: Character scalar. Add annotation
information as group labels. This can be a value in id, group
or feature. Defaults to group. Only works if showId is
not FALSE.
just.group="left": Character scalar. the justification of
group labels. Either left, right, above or
below.
lex=1: Numeric scalar. The line expansion factor for all
track items. This is also used to connect grouped items. See
grouping for details.
lineheight=1: Numeric scalar. The font line height for item
identifiers.
lty="solid": Character or integer scalar. The line type for
all track items. This is also used to connect grouped items. See
grouping for details.
lwd=1: Integer scalar. The line width for all track items.
This is also used to connect grouped items. See grouping for
details.
mergeGroups=FALSE: Logical scalar. Merge fully overlapping
groups if collapse==TRUE.
min.height=3: Numeric scalar. The minimum range height in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details. For feathered
bars indicating the strandedness of grouped items this also controls the
height of the arrow feathers.
min.width=1: Numeric scalar. The minimum range width in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
rotation=0: Numeric scalar. The degree of text rotation for
item identifiers.
rotation.group=0: Numeric scalar. The degree of text rotation
for group labels.
rotation.item=0: Numeric scalar. The degree of text rotation
for item identifiers.
shape="arrow": Character scalar. The shape in which to
display the track items. Currently only box, arrow,
fixedArrow, ellipse, and smallArrow are implemented.
showFeatureId=FALSE: Logical scalar. Control whether to plot
the individual track item identifiers.
showId=FALSE: Logical scalar. Control whether to annotate
individual groups.
showOverplotting=FALSE: Logical scalar. Use a color gradient
to show the amount of overplotting for collapsed items. This implies that
collapse==TRUE
size=1: Numeric scalar. The relative size of the track. Can
be overridden in the plotTracks function.
Inherited from class StackedTrack:
stackHeight=0.75: Numeric between 0 and 1. Controls the
vertical size and spacing between stacked elements. The number defines the
proportion of the total available space for the stack that is used to draw
the glyphs. E.g., a value of 0.5 means that half of the available vertical
drawing space (for each stacking line) is used for the glyphs, and thus one
quarter of the available space each is used for spacing above and below the
glyph. Defaults to 0.75.
reverseStacking=FALSE: Logical flag. Reverse the y-ordering
of stacked items. I.e., features that are plotted on the bottom-most stacks
will be moved to the top-most stack and vice versa.
Inherited from class GdObject:
alpha=1: Numeric scalar. The transparency for all track
items.
alpha.title=NULL: Numeric scalar. The transparency for the
title panel.
background.panel="transparent": Integer or character scalar.
The background color of the content panel.
background.title="lightgray": Integer or character scalar.
The background color for the title panel.
background.legend="transparent": Integer or character scalar.
The background color for the legend.
cex.axis=NULL: Numeric scalar. The expansion factor for the
axis annotation. Defaults to NULL, in which case it is automatically
determined based on the available space.
cex.title=NULL: Numeric scalar. The expansion factor for the
title panel. This effects the fontsize of both the title and the axis, if
any. Defaults to NULL, which means that the text size is
automatically adjusted to the available space.
col.axis="white": Integer or character scalar. The font and
line color for the y axis, if any.
col.border.title="white": Integer or character scalar. The
border color for the title panels.
col.frame="lightgray": Integer or character scalar. The line
color used for the panel frame, if frame==TRUE
col.grid="#808080": Integer or character scalar. Default
line color for grid lines, both when type=="g" in
DataTracks and when display parameter grid==TRUE.
col.symbol=NULL: Integer or character scalar. Default colors
for plot symbols. Usually the same as the global col parameter.
col.title="white": Integer or character scalar. The border
color for the title panels
collapse=TRUE: Boolean controlling whether to collapse the
content of the track to accomodate the minimum current device resolution.
See collapsing for details.
fontcolor="black": Integer or character scalar. The font
color for all text, unless a more specific definition exists.
fontface.title=2: Integer or character scalar. The font face
for the title panels.
fontface=1: Integer or character scalar. The font face for
all text, unless a more specific definition exists.
fontfamily.title="sans": Integer or character scalar. The
font family for the title panels.
fontfamily="sans": Integer or character scalar. The font
family for all text, unless a more specific definition exists.
fontsize=12: Numeric scalar. The font size for all text,
unless a more specific definition exists.
frame=FALSE: Boolean. Draw a frame around the track when
plotting.
grid=FALSE: Boolean, switching on/off the plotting of a
grid.
h=-1: Integer scalar. Parameter controlling the number of
horizontal grid lines, see panel.grid for details.
lty.grid="solid": Integer or character scalar. Default line
type for grid lines, both when type=="g" in DataTracks
and when display parameter grid==TRUE.
lwd.border.title=1: Integer scalar. The border width for the
title panels.
lwd.title=1: Integer scalar. The border width for the title
panels
lwd.grid=1: Numeric scalar. Default line width for grid
lines, both when type=="g" in DataTracks and when
display parameter grid==TRUE.
min.distance=1: Numeric scalar. The minimum pixel distance
before collapsing range items, only if collapse==TRUE. See
collapsing for details.
reverseStrand=FALSE: Logical scalar. Set up the plotting
coordinates in 3' -> 5' direction if TRUE. This will effectively
mirror the plot on the vertical axis.
rotation.title=90: The rotation angle for the text in the
title panel. Even though this can be adjusted, the automatic resizing of the
title panel will currently not work, so use at own risk.
showAxis=TRUE: Boolean controlling whether to plot a y axis
(only applies to track types where axes are implemented).
showTitle=TRUE: Boolean controlling whether to plot a title
panel. Although this can be set individually for each track, in multi-track
plots as created by plotTracks there will still be an empty
placeholder in case any of the other tracks include a title. The same holds
true for axes. Note that the the title panel background color could be set
to transparent in order to completely hide it.
v=-1: Integer scalar. Parameter controlling the number of
vertical grid lines, see panel.grid for details.
- GeneRegionTrack:
-
arrowHeadWidth=10: Numeric scalar. The width of the arrow
head in pixels if shape is fixedArrow.
arrowHeadMaxWidth=20: Numeric scalar. The maximum width of
the arrow head in pixels if shape is arrow.
col=NULL: Character or integer scalar. The border color for
all track items. Defaults to using the same color as in fill, also
taking into account different track features.
collapseTranscripts=FALSE: Logical or character scalar. Can
be one in gene, longest, shortest or meta. Merge
all transcripts of the same gene into one single gene model. In the case of
gene (or TRUE), this will only keep the start location of the
first exon and the end location of the last exon from all transcripts of the
gene. For shortest and longest, only the longest or shortest
transcript model is retained. For meta, a meta-transcript containing
the union of all exons is formed (essentially identical to the operation
reduce(geneModel)).
exonAnnotation=NULL: Character scalar. Add annotation
information to the individual exon models. This can be a value in
symbol, gene, transcript, exon or
feature. Defaults to exon. Only works if showExonId is
not FALSE.
fill="orange": Character or integer scalar. The fill color
for untyped items. This is also used to connect grouped items. See
grouping for details.
min.distance=0: Numeric scalar. The minimum pixel distance
before collapsing range items, only if collapse==TRUE. See
collapsing for details. Note that a value larger than 0 may
lead to UTR regions being merged to CDS regions, which in most cases is not
particularly useful.
shape=c("smallArrow", "box"): Character scalar. The shape in
which to display the track items. Currently only box, arrow,
ellipse, and smallArrow are implemented.
showExonId=NULL: Logical scalar. Control whether to plot the
individual exon identifiers.
thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5", "3UTR",
"5UTR", "miRNA", "lincRNA", "three_prime_UTR", "five_prime_UTR"): Character
vector. A listing of feature types that should be drawn with thin boxes.
Typically those are non-coding elements.
transcriptAnnotation=NULL: Character scalar. Add annotation
information as transcript labels. This can be a value in symbol,
gene, transcript, exon or feature. Defaults to
symbol. Only works if showId is not FALSE.
Inherited from class AnnotationTrack:
cex.group=0.6: Numeric scalar. The font expansion factor for
the group-level annotation.
cex=1: Numeric scalar. The font expansion factor for item
identifiers.
col.line="darkgray": Character scalar. The color used for
connecting lines between grouped items. Defaults to a light gray, but if set
to NULL the same color as for the first item in the group is used.
featureAnnotation=NULL: Character scalar. Add annotation
information to the individual track elements. This can be a value in
id, group or feature. Defaults to id. Only
works if showFeatureId is not FALSE.
fontfamily.group="sans": Character scalar. The font family
for the group-level annotation.
fontcolor.group="#808080": Character or integer scalar. The
font color for the group-level annotation.
fontcolor.item="white": Character or integer scalar. The font
color for item identifiers.
fontface.group=2: Numeric scalar. The font face for the
group-level annotation.
fontsize.group=12: Numeric scalar. The font size for the
group-level annotation.
groupAnnotation=NULL: Character scalar. Add annotation
information as group labels. This can be a value in id, group
or feature. Defaults to group. Only works if showId is
not FALSE.
just.group="left": Character scalar. the justification of
group labels. Either left, right, above or
below.
lex=1: Numeric scalar. The line expansion factor for all
track items. This is also used to connect grouped items. See
grouping for details.
lineheight=1: Numeric scalar. The font line height for item
identifiers.
lty="solid": Character or integer scalar. The line type for
all track items. This is also used to connect grouped items. See
grouping for details.
lwd=1: Integer scalar. The line width for all track items.
This is also used to connect grouped items. See grouping for
details.
mergeGroups=FALSE: Logical scalar. Merge fully overlapping
groups if collapse==TRUE.
min.height=3: Numeric scalar. The minimum range height in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details. For feathered
bars indicating the strandedness of grouped items this also controls the
height of the arrow feathers.
min.width=1: Numeric scalar. The minimum range width in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
rotation=0: Numeric scalar. The degree of text rotation for
item identifiers.
rotation.group=0: Numeric scalar. The degree of text rotation
for group labels.
rotation.item=0: Numeric scalar. The degree of text rotation
for item identifiers.
showFeatureId=FALSE: Logical scalar. Control whether to plot
the individual track item identifiers.
showId=FALSE: Logical scalar. Control whether to annotate
individual groups.
showOverplotting=FALSE: Logical scalar. Use a color gradient
to show the amount of overplotting for collapsed items. This implies that
collapse==TRUE
size=1: Numeric scalar. The relative size of the track. Can
be overridden in the plotTracks function.
Inherited from class StackedTrack:
stackHeight=0.75: Numeric between 0 and 1. Controls the
vertical size and spacing between stacked elements. The number defines the
proportion of the total available space for the stack that is used to draw
the glyphs. E.g., a value of 0.5 means that half of the available vertical
drawing space (for each stacking line) is used for the glyphs, and thus one
quarter of the available space each is used for spacing above and below the
glyph. Defaults to 0.75.
reverseStacking=FALSE: Logical flag. Reverse the y-ordering
of stacked items. I.e., features that are plotted on the bottom-most stacks
will be moved to the top-most stack and vice versa.
Inherited from class GdObject:
alpha=1: Numeric scalar. The transparency for all track
items.
alpha.title=NULL: Numeric scalar. The transparency for the
title panel.
background.panel="transparent": Integer or character scalar.
The background color of the content panel.
background.title="lightgray": Integer or character scalar.
The background color for the title panel.
background.legend="transparent": Integer or character scalar.
The background color for the legend.
cex.axis=NULL: Numeric scalar. The expansion factor for the
axis annotation. Defaults to NULL, in which case it is automatically
determined based on the available space.
cex.title=NULL: Numeric scalar. The expansion factor for the
title panel. This effects the fontsize of both the title and the axis, if
any. Defaults to NULL, which means that the text size is
automatically adjusted to the available space.
col.axis="white": Integer or character scalar. The font and
line color for the y axis, if any.
col.border.title="white": Integer or character scalar. The
border color for the title panels.
col.frame="lightgray": Integer or character scalar. The line
color used for the panel frame, if frame==TRUE
col.grid="#808080": Integer or character scalar. Default
line color for grid lines, both when type=="g" in
DataTracks and when display parameter grid==TRUE.
col.symbol=NULL: Integer or character scalar. Default colors
for plot symbols. Usually the same as the global col parameter.
col.title="white": Integer or character scalar. The border
color for the title panels
collapse=TRUE: Boolean controlling whether to collapse the
content of the track to accomodate the minimum current device resolution.
See collapsing for details.
fontcolor="black": Integer or character scalar. The font
color for all text, unless a more specific definition exists.
fontface.title=2: Integer or character scalar. The font face
for the title panels.
fontface=1: Integer or character scalar. The font face for
all text, unless a more specific definition exists.
fontfamily.title="sans": Integer or character scalar. The
font family for the title panels.
fontfamily="sans": Integer or character scalar. The font
family for all text, unless a more specific definition exists.
fontsize=12: Numeric scalar. The font size for all text,
unless a more specific definition exists.
frame=FALSE: Boolean. Draw a frame around the track when
plotting.
grid=FALSE: Boolean, switching on/off the plotting of a
grid.
h=-1: Integer scalar. Parameter controlling the number of
horizontal grid lines, see panel.grid for details.
lty.grid="solid": Integer or character scalar. Default line
type for grid lines, both when type=="g" in DataTracks
and when display parameter grid==TRUE.
lwd.border.title=1: Integer scalar. The border width for the
title panels.
lwd.title=1: Integer scalar. The border width for the title
panels
lwd.grid=1: Numeric scalar. Default line width for grid
lines, both when type=="g" in DataTracks and when
display parameter grid==TRUE.
reverseStrand=FALSE: Logical scalar. Set up the plotting
coordinates in 3' -> 5' direction if TRUE. This will effectively
mirror the plot on the vertical axis.
rotation.title=90: The rotation angle for the text in the
title panel. Even though this can be adjusted, the automatic resizing of the
title panel will currently not work, so use at own risk.
showAxis=TRUE: Boolean controlling whether to plot a y axis
(only applies to track types where axes are implemented).
showTitle=TRUE: Boolean controlling whether to plot a title
panel. Although this can be set individually for each track, in multi-track
plots as created by plotTracks there will still be an empty
placeholder in case any of the other tracks include a title. The same holds
true for axes. Note that the the title panel background color could be set
to transparent in order to completely hide it.
v=-1: Integer scalar. Parameter controlling the number of
vertical grid lines, see panel.grid for details.
- BiomartGeneRegionTrack:
-
C_segment="burlywood4": Character or integer scalar. Fill
color for annotation objects of type 'C_segment'.
D_segment="lightblue": Character or integer scalar. Fill
color for annotation objects of type 'C_segment'.
J_segment="dodgerblue2": Character or integer scalar. Fill
color for annotation objects of type 'C_segment'.
Mt_rRNA="yellow": Character or integer scalar. Fill color
for annotation objects of type 'Mt_rRNA'.
Mt_tRNA="darkgoldenrod": Character or integer scalar. Fill
color for annotation objects of type 'Mt_tRNA'.
Mt_tRNA_pseudogene="darkgoldenrod1": Character or integer
scalar. Fill color for annotation objects of type 'Mt_tRNA_pseudogene'.
V_segment="aquamarine": Character or integer scalar. Fill
color for annotation objects of type 'V_segment'.
miRNA="cornflowerblue": Character or integer scalar. Fill
color for annotation objects of type 'L_segment'.
miRNA_pseudogene="cornsilk": Character or integer scalar.
Fill color for annotation objects of type 'miRNA_pseudogene'.
misc_RNA="cornsilk3": Character or integer scalar. Fill color
for annotation objects of type 'misc_RNA'.
misc_RNA_pseudogene="cornsilk4": Character or integer scalar.
Fill color for annotation objects of type 'misc_RNA_pseudogene'.
protein_coding="#FFD58A": Character or integer scalar. Fill
color for annotation objects of type 'protein_coding'.
pseudogene="brown1": Character or integer scalar. Fill color
for annotation objects of type 'pseudogene'.
rRNA="darkolivegreen1": Character or integer scalar. Fill
color for annotation objects of type 'rRNA'.
rRNA_pseudogene="darkolivegreen": Character or integer
scalar. Fill color for annotation objects of type 'rRNA_pseudogene'.
retrotransposed="blueviolet": Character or integer scalar.
Fill color for annotation objects of type 'retrotransposed'.
scRNA="gold4": Character or integer scalar. Fill color for
annotation objects of type 'scRNA'.
scRNA_pseudogene="darkorange2": Character or integer scalar.
Fill color for annotation objects of type 'scRNA_pseudogene'.
snRNA="coral": Character or integer scalar. Fill color for
annotation objects of type 'snRNA'.
snRNA_pseudogene="coral3": Character or integer scalar. Fill
color for annotation objects of type 'snRNA_pseudogene'.
snoRNA="cyan": Character or integer scalar. Fill color for
annotation objects of type 'snoRNA'.
snoRNA_pseudogene="cyan2": Character or integer scalar. Fill
color for annotation objects of type 'snoRNA_pseudogene'.
tRNA_pseudogene="antiquewhite3": Character or integer scalar.
Fill color for annotation objects of type 'tRNA_pseudogene'.
utr3="#FFD58A": Character or integer scalar. Fill color for
annotation objects of type 'utr3'.
utr5="#FFD58A": Character or integer scalar. Fill color for
annotation objects of type 'utr5'.
verbose=FALSE: Logical scalar. Report data loading events
from Bioamart or retrieval from cache.
Inherited from class GeneRegionTrack:
arrowHeadWidth=10: Numeric scalar. The width of the arrow
head in pixels if shape is fixedArrow.
arrowHeadMaxWidth=20: Numeric scalar. The maximum width of
the arrow head in pixels if shape is arrow.
col=NULL: Character or integer scalar. The border color for
all track items. Defaults to using the same color as in fill, also
taking into account different track features.
collapseTranscripts=FALSE: Logical or character scalar. Can
be one in gene, longest, shortest or meta. Merge
all transcripts of the same gene into one single gene model. In the case of
gene (or TRUE), this will only keep the start location of the
first exon and the end location of the last exon from all transcripts of the
gene. For shortest and longest, only the longest or shortest
transcript model is retained. For meta, a meta-transcript containing
the union of all exons is formed (essentially identical to the operation
reduce(geneModel)).
exonAnnotation=NULL: Character scalar. Add annotation
information to the individual exon models. This can be a value in
symbol, gene, transcript, exon or
feature. Defaults to exon. Only works if showExonId is
not FALSE.
fill="orange": Character or integer scalar. The fill color
for untyped items. This is also used to connect grouped items. See
grouping for details.
min.distance=0: Numeric scalar. The minimum pixel distance
before collapsing range items, only if collapse==TRUE. See
collapsing for details. Note that a value larger than 0 may
lead to UTR regions being merged to CDS regions, which in most cases is not
particularly useful.
shape=c("smallArrow", "box"): Character scalar. The shape in
which to display the track items. Currently only box, arrow,
ellipse, and smallArrow are implemented.
showExonId=NULL: Logical scalar. Control whether to plot the
individual exon identifiers.
thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5", "3UTR",
"5UTR", "miRNA", "lincRNA", "three_prime_UTR", "five_prime_UTR"): Character
vector. A listing of feature types that should be drawn with thin boxes.
Typically those are non-coding elements.
transcriptAnnotation=NULL: Character scalar. Add annotation
information as transcript labels. This can be a value in symbol,
gene, transcript, exon or feature. Defaults to
symbol. Only works if showId is not FALSE.
Inherited from class AnnotationTrack:
cex.group=0.6: Numeric scalar. The font expansion factor for
the group-level annotation.
cex=1: Numeric scalar. The font expansion factor for item
identifiers.
col.line="darkgray": Character scalar. The color used for
connecting lines between grouped items. Defaults to a light gray, but if set
to NULL the same color as for the first item in the group is used.
featureAnnotation=NULL: Character scalar. Add annotation
information to the individual track elements. This can be a value in
id, group or feature. Defaults to id. Only
works if showFeatureId is not FALSE.
fontfamily.group="sans": Character scalar. The font family
for the group-level annotation.
fontcolor.group="#808080": Character or integer scalar. The
font color for the group-level annotation.
fontcolor.item="white": Character or integer scalar. The font
color for item identifiers.
fontface.group=2: Numeric scalar. The font face for the
group-level annotation.
fontsize.group=12: Numeric scalar. The font size for the
group-level annotation.
groupAnnotation=NULL: Character scalar. Add annotation
information as group labels. This can be a value in id, group
or feature. Defaults to group. Only works if showId is
not FALSE.
just.group="left": Character scalar. the justification of
group labels. Either left, right, above or
below.
lex=1: Numeric scalar. The line expansion factor for all
track items. This is also used to connect grouped items. See
grouping for details.
lineheight=1: Numeric scalar. The font line height for item
identifiers.
lty="solid": Character or integer scalar. The line type for
all track items. This is also used to connect grouped items. See
grouping for details.
lwd=1: Integer scalar. The line width for all track items.
This is also used to connect grouped items. See grouping for
details.
mergeGroups=FALSE: Logical scalar. Merge fully overlapping
groups if collapse==TRUE.
min.height=3: Numeric scalar. The minimum range height in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details. For feathered
bars indicating the strandedness of grouped items this also controls the
height of the arrow feathers.
min.width=1: Numeric scalar. The minimum range width in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
rotation=0: Numeric scalar. The degree of text rotation for
item identifiers.
rotation.group=0: Numeric scalar. The degree of text rotation
for group labels.
rotation.item=0: Numeric scalar. The degree of text rotation
for item identifiers.
showFeatureId=FALSE: Logical scalar. Control whether to plot
the individual track item identifiers.
showId=FALSE: Logical scalar. Control whether to annotate
individual groups.
showOverplotting=FALSE: Logical scalar. Use a color gradient
to show the amount of overplotting for collapsed items. This implies that
collapse==TRUE
size=1: Numeric scalar. The relative size of the track. Can
be overridden in the plotTracks function.
Inherited from class StackedTrack:
stackHeight=0.75: Numeric between 0 and 1. Controls the
vertical size and spacing between stacked elements. The number defines the
proportion of the total available space for the stack that is used to draw
the glyphs. E.g., a value of 0.5 means that half of the available vertical
drawing space (for each stacking line) is used for the glyphs, and thus one
quarter of the available space each is used for spacing above and below the
glyph. Defaults to 0.75.
reverseStacking=FALSE: Logical flag. Reverse the y-ordering
of stacked items. I.e., features that are plotted on the bottom-most stacks
will be moved to the top-most stack and vice versa.
Inherited from class GdObject:
alpha=1: Numeric scalar. The transparency for all track
items.
alpha.title=NULL: Numeric scalar. The transparency for the
title panel.
background.panel="transparent": Integer or character scalar.
The background color of the content panel.
background.title="lightgray": Integer or character scalar.
The background color for the title panel.
background.legend="transparent": Integer or character scalar.
The background color for the legend.
cex.axis=NULL: Numeric scalar. The expansion factor for the
axis annotation. Defaults to NULL, in which case it is automatically
determined based on the available space.
cex.title=NULL: Numeric scalar. The expansion factor for the
title panel. This effects the fontsize of both the title and the axis, if
any. Defaults to NULL, which means that the text size is
automatically adjusted to the available space.
col.axis="white": Integer or character scalar. The font and
line color for the y axis, if any.
col.border.title="white": Integer or character scalar. The
border color for the title panels.
col.frame="lightgray": Integer or character scalar. The line
color used for the panel frame, if frame==TRUE
col.grid="#808080": Integer or character scalar. Default
line color for grid lines, both when type=="g" in
DataTracks and when display parameter grid==TRUE.
col.symbol=NULL: Integer or character scalar. Default colors
for plot symbols. Usually the same as the global col parameter.
col.title="white": Integer or character scalar. The border
color for the title panels
collapse=TRUE: Boolean controlling whether to collapse the
content of the track to accomodate the minimum current device resolution.
See collapsing for details.
fontcolor="black": Integer or character scalar. The font
color for all text, unless a more specific definition exists.
fontface.title=2: Integer or character scalar. The font face
for the title panels.
fontface=1: Integer or character scalar. The font face for
all text, unless a more specific definition exists.
fontfamily.title="sans": Integer or character scalar. The
font family for the title panels.
fontfamily="sans": Integer or character scalar. The font
family for all text, unless a more specific definition exists.
fontsize=12: Numeric scalar. The font size for all text,
unless a more specific definition exists.
frame=FALSE: Boolean. Draw a frame around the track when
plotting.
grid=FALSE: Boolean, switching on/off the plotting of a
grid.
h=-1: Integer scalar. Parameter controlling the number of
horizontal grid lines, see panel.grid for details.
lty.grid="solid": Integer or character scalar. Default line
type for grid lines, both when type=="g" in DataTracks
and when display parameter grid==TRUE.
lwd.border.title=1: Integer scalar. The border width for the
title panels.
lwd.title=1: Integer scalar. The border width for the title
panels
lwd.grid=1: Numeric scalar. Default line width for grid
lines, both when type=="g" in DataTracks and when
display parameter grid==TRUE.
reverseStrand=FALSE: Logical scalar. Set up the plotting
coordinates in 3' -> 5' direction if TRUE. This will effectively
mirror the plot on the vertical axis.
rotation.title=90: The rotation angle for the text in the
title panel. Even though this can be adjusted, the automatic resizing of the
title panel will currently not work, so use at own risk.
showAxis=TRUE: Boolean controlling whether to plot a y axis
(only applies to track types where axes are implemented).
showTitle=TRUE: Boolean controlling whether to plot a title
panel. Although this can be set individually for each track, in multi-track
plots as created by plotTracks there will still be an empty
placeholder in case any of the other tracks include a title. The same holds
true for axes. Note that the the title panel background color could be set
to transparent in order to completely hide it.
v=-1: Integer scalar. Parameter controlling the number of
vertical grid lines, see panel.grid for details.
- AlignmentsTrack:
-
alpha.reads=0.5: Numeric scalar between 0 and 1. The
transparency of the individual read icons. Can be used to indicate
overlapping regions in read pairs. Only on supported devices.
alpha.mismatch=1: Numeric scalar between 0 and 1. The
transparency of the mismatch base information.
cex=0.7: Numeric Scalar. The global character expansion
factor.
cex.mismatch=NULL: Numeric Scalar. The character expansion
factor for the mismatch base letters.
col.coverage=NULL: Integer or character scalar. The line
color for the coverage profile.
col.gap="#808080": Integer or character scalar. The color of
the line that is bridging the gap regions in gapped alignments.
col.mates="#E0E0E0": Integer or character scalar. The color
of the line that is connecting two paired reads.
col.deletion="#000000": Integer or character scalar. The
color of the line that is bridging the deleted regions in alignments.
col.insertion="#984EA3": Integer or character scalar. The
color of the line that highlighting insertions in alignments.
col.mismatch="#808080": Integer or character scalar. The box
color around mismatch bases.
col.reads=NULL: Integer or character scalar. The box color
around reads.
col.sashimi=NULL: Integer or character scalar. The line
color for sashimi plots.
col="#808080": Integer or character scalar. The default color
of all line elements.
collapse=FALSE: Logical scalar. Do not perform any collapsing
of overlapping elements. Currently not supported.
coverageHeight=0.1: Numeric scalar. The height of the
coverage region of the track. Can either be a value between 0 and 1 in which
case it is taken as a relative height, or a positive value greater 1 in
which case it is interpreted as pixels.
fill.coverage=NULL: Integer or character scalar. The fill
color for the coverage profile.
fill.reads=NULL: Integer or character scalar. The fill color
for the read icons.
fill="#BABABA": Integer or character scalar. The default
fill color of all plot elements.
fontface.mismatch=2: Integer scalar. The font face for
mismatch bases.
lty.coverage=NULL: Integer or character scalar. The line
type of the coverage profile.
lty.gap=NULL: Integer or character scalar. The type of the
line that is bridging the gap regions in gapped alignments.
lty.mates=NULL: Integer or character scalar. The type of the
line that is connecting two paired reads.
lty.deletion=NULL: Integer or character scalar. The type of
the line that is bridging the deleted regions in alignments.
lty.insertion=NULL: Integer or character scalar. The type of
the line that highlighting insertions in alignments.
lty.mismatch=NULL: Integer or character scalar. The box line
type around mismatch bases.
lty.reads=NULL: Integer or character scalar. The box line
type around mismatch reads.
lty=1: Integer or character scalar. The default type of all
line elements.
lwd.coverage=NULL: Integer or character scalar. The line
width of the coverage profile.
lwd.gap=NULL: Integer scalar. The width of the line that is
bridging the gap regions in gapped alignments.
lwd.mates=NULL: Integer scalar. The width of the line that is
connecting two paired reads.
lwd.deletion=NULL: Integer scalar. The width of the line that
is bridging the deleted regions in alignments.
lwd.insertion=NULL: Integer scalar. The width of the line
that highlighting insertions in alignments.
lwd.mismatch=NULL: Integer scalar. The box line width around
mismatch bases.
lwd.reads=NULL: Integer scalar. The box line width around
reads.
lwd.sashimiMax=10: Integer scalar. The maximal width of the
line in sashimi plots.
lwd=1: Integer scalar. The default width of all line
elements.
max.height=10: Integer scalar. The maximum height of an
individual read in pixels. Can be used in combination with min.height
to control the read and stacking appearance.
min.height=5: Integer scalar. The minimum height of an
individual read in pixels. Can be used in combination with max.height
to control the read and stacking appearance.
minCoverageHeight=50: Integer scalar. The minimum height of
the coverage section. Uselful in combination with a relative setting of
coverageHeight.
minSashimiHeight=50: Integer scalar. The minimum height of
the sashimi section. Uselful in combination with a relative setting of
sashimiHeight.
noLetters=FALSE: Logical scalar. Always plot colored boxes
for mismatch bases regardles of the available space.
sashimiFilter=NULL: GRanges object. Only junctions which
overlap equally with sashimiFilter GRanges are shown. Default
NULL, no filtering.
sashimiFilterTolerance=0: Integer scalar. Only used in
combination with sashimiFilter. It allows to include junctions whose
starts/ends are within specified distance from sashimiFilter GRanges.
This is useful for cases where the aligner did not place the junction reads
precisely. Default 0L , no tolerance.
sashimiHeight=0.1: Integer scalar. The height of the sashimi
part of the track. Can either be a value between 0 and 1 in which case it is
taken as a relative height, or a positive value greater 1 in which case it
is interpreted as pixels.
sashimiScore=1: Integer scalar. The minimum number of reads
supporting the junction.
sashimiStrand="*": Integer scalar. Only reads which have the
specified strand are considered to count the junctions.
sashimiTransformation=NULL: Function. Applied to the junction
score vector prior to plotting. The function should accept exactly one input
argument and its return value needs to be a numeric vector of identical
length as the input data.
showIndels=FALSE: Logical scalar. Consider insertions and
deletions in coverage and pile-up. Default is FALSE. If set to
TRUE the deletions defined in CIGAR string are not considered in
coverage plot. The deletions are displayed as bridging lines in pile-up
track. Insertions are shown as vertical bars.
showMismatches=TRUE: Logical scalar. Add mismatch
information, either as individual base letters or using color coded bars.
This implies that the reference sequence has been provided, either to the
class constructor or as part of the track list.
size=NULL: Numeric scalar. The size of the track. Defaults
to automatic sizing.
transformation=NULL: Function. Applied to the coverage vector
prior to plotting. The function should accept exactly one input argument and
its return value needs to be a numeric Rle of identical length as the input
data.
type=c("coverage", "pileup"): Character vactor. The type of
information to plot. For coverage a coverage plot, potentially
augmented by base mismatch information, for sashimi a sashimi plot,
showing the juctions, and for pileup the pileups of the individual
reads. These three can be combined.
Inherited from class StackedTrack:
stackHeight=0.75: Numeric between 0 and 1. Controls the
vertical size and spacing between stacked elements. The number defines the
proportion of the total available space for the stack that is used to draw
the glyphs. E.g., a value of 0.5 means that half of the available vertical
drawing space (for each stacking line) is used for the glyphs, and thus one
quarter of the available space each is used for spacing above and below the
glyph. Defaults to 0.75.
reverseStacking=FALSE: Logical flag. Reverse the y-ordering
of stacked items. I.e., features that are plotted on the bottom-most stacks
will be moved to the top-most stack and vice versa.
Inherited from class GdObject:
alpha=1: Numeric scalar. The transparency for all track
items.
alpha.title=NULL: Numeric scalar. The transparency for the
title panel.
background.panel="transparent": Integer or character scalar.
The background color of the content panel.
background.title="lightgray": Integer or character scalar.
The background color for the title panel.
background.legend="transparent": Integer or character scalar.
The background color for the legend.
cex.axis=NULL: Numeric scalar. The expansion factor for the
axis annotation. Defaults to NULL, in which case it is automatically
determined based on the available space.
cex.title=NULL: Numeric scalar. The expansion factor for the
title panel. This effects the fontsize of both the title and the axis, if
any. Defaults to NULL, which means that the text size is
automatically adjusted to the available space.
col.axis="white": Integer or character scalar. The font and
line color for the y axis, if any.
col.border.title="white": Integer or character scalar. The
border color for the title panels.
col.frame="lightgray": Integer or character scalar. The line
color used for the panel frame, if frame==TRUE
col.grid="#808080": Integer or character scalar. Default
line color for grid lines, both when type=="g" in
DataTracks and when display parameter grid==TRUE.
col.line=NULL: Integer or character scalar. Default colors
for plot lines. Usually the same as the global col parameter.
col.symbol=NULL: Integer or character scalar. Default colors
for plot symbols. Usually the same as the global col parameter.
col.title="white": Integer or character scalar. The border
color for the title panels
fontcolor="black": Integer or character scalar. The font
color for all text, unless a more specific definition exists.
fontface.title=2: Integer or character scalar. The font face
for the title panels.
fontface=1: Integer or character scalar. The font face for
all text, unless a more specific definition exists.
fontfamily.title="sans": Integer or character scalar. The
font family for the title panels.
fontfamily="sans": Integer or character scalar. The font
family for all text, unless a more specific definition exists.
fontsize=12: Numeric scalar. The font size for all text,
unless a more specific definition exists.
frame=FALSE: Boolean. Draw a frame around the track when
plotting.
grid=FALSE: Boolean, switching on/off the plotting of a
grid.
h=-1: Integer scalar. Parameter controlling the number of
horizontal grid lines, see panel.grid for details.
lineheight=1: Numeric scalar. The font line height for all
text, unless a more specific definition exists.
lty.grid="solid": Integer or character scalar. Default line
type for grid lines, both when type=="g" in DataTracks
and when display parameter grid==TRUE.
lwd.border.title=1: Integer scalar. The border width for the
title panels.
lwd.title=1: Integer scalar. The border width for the title
panels
lwd.grid=1: Numeric scalar. Default line width for grid
lines, both when type=="g" in DataTracks and when
display parameter grid==TRUE.
min.distance=1: Numeric scalar. The minimum pixel distance
before collapsing range items, only if collapse==TRUE. See
collapsing for details.
min.width=1: Numeric scalar. The minimum range width in
pixels to display. All ranges are expanded to this size in order to avoid
rendering issues. See collapsing for details.
reverseStrand=FALSE: Logical scalar. Set up the plotting
coordinates in 3' -> 5' direction if TRUE. This will effectively
mirror the plot on the vertical axis.
rotation.title=90: The rotation angle for the text in the
title panel. Even though this can be adjusted, the automatic resizing of the
title panel will currently not work, so use at own risk.
rotation=0: The rotation angle for all text unless a more
specific definiton exists.
showAxis=TRUE: Boolean controlling whether to plot a y axis
(only applies to track types where axes are implemented).
showTitle=TRUE: Boolean controlling whether to plot a title
panel. Although this can be set individually for each track, in multi-track
plots as created by plotTracks there will still be an empty
placeholder in case any of the other tracks include a title. The same holds
true for axes. Note that the the title panel background color could be set
to transparent in order to completely hide it.
v=-1: Integer scalar. Parameter controlling the number of
vertical grid lines, see panel.grid for details.
Author(s)
Florian Hahne
See Also
AnnotationTrack
DataTrack
DisplayPars
GdObject
availableDisplayPars
collapsing
grouping
horizonplot
panel.bwplot
panel.grid
panel.loess
panel.xyplot
plotTracks
Examples
## Which scheme is used?
getOption("Gviz.scheme")
## Change default settings for GeneRegionTrack
scheme <- getScheme()
scheme$GeneRegionTrack$fill <- "salmon"
scheme$GeneRegionTrack$col <- NULL
scheme$GeneRegionTrack$transcriptAnnotation <- "transcript"
## replace default scheme with myScheme
addScheme(scheme, "myScheme")
options(Gviz.scheme = "myScheme")
getOption("Gviz.scheme")
data(geneModels)
grtrack <- GeneRegionTrack(geneModels, genome = "hg19", chromosome = "chr7", name = "Gene Model")
plotTracks(grtrack)
ivanek/Gviz documentation built on Nov. 20, 2023, 8:16 p.m.
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| settings | R Documentation |
Setting display parameters to control the look and feel of the plots
Description
The genome track plots in this package are all highly customizable by means of so called 'display parameters'. This page highlights the use of these parameters and list all available settings for the different track classes.
Arguments
scheme |
A named nested list of display parameters, where the first level of nesting represents Gviz track object classes, and the second level of nesting represents parameters. |
name |
A character scalar with the scheme name. |
Details
All of the package's track objects inherit the dp slot from the
GdObject parent class, which is the main container to
store an object's display parameters. Internally, the content of this slot
has to be an object of class DisplayPars, but the user
is usually not exposed to this low level implementation. Instead, there are
two main interaction points, namely the individual object constructor
functions and the final plotTracks function. In both cases,
all additional arguments that are not caught by any of the formally defined
function parameters are being interpreted as additional display parameters
and are automatically added to the aforementioned slot. The main difference
here is that display parameters that are passed on to the constructor
function are specific for an individual track object, whereas those supplied
to the plotTracks function will be applied to all the objects in the
plotting list. Not all display parameters have an effect on the plotting of
all track classes, and those will be silently ignored.
One can query the available display parameters for a given class as well as
their default values by calling the availableDisplayPars
function, or by inspecting the man pages of the individual track classes.
The structure of the classes defined in this package is hierarchical, and so
are the available display parameters, i.e., all objects inherit the
parameters defined in the commom GdObject parent class, and so on.
Once a track object has been created, the display parameters are still open
for modification. To this end, the DisplayPars replacement
method is available for all objects inheriting from class GdObject.
The method takes a named list of parameters as input, e.g.:
displayPars(foo) <- list(col="red", lwd=2)
In the same spirit, the currently set display parameters for the object
foo can be inferred using the displayPars method directly,
e.g.:
displayPars(foo)
For track objects inheriting from class
AnnotationTrack, display parameters that are not
formally defined in the class definition or in any of the parent classes are
considered to be valid R color identifiers that are used to distinguish
between different types of annotation features. For instance, the parameter
'miRNA' will be used to color all annotation features of class miRNA. The
annotation types can be set in the constructor function of the track object
via the feature argument. For most of the tracks that have been
inferred from one of the online repositories, this classification will
usually be downloaded along with the actual annotation data.
Users might find themselves changing the same parameters over and over
again, and it would make sense to register these modifications in a central
location once and for all. To this end the Gviz package supports display
parameter schemes. A scheme is essentially just a bunch of nested named
lists, where the names on the first level of nesting should correspond to
track class names, and the names on the second level to the display
parameters to set. The currently active schmeme can be changed by setting
the global option Gviz.scheme, and a new scheme can be registered by
using the addScheme function, providing both the list and the name
for the new scheme. The getScheme function is useful to get the
current scheme as a list structure, for instance to use as a skeleton for
your own custom scheme.
In order to make these settings persitant across R sessions one can create
one or several schemes in the global environment in the special object
.GvizSchemes, for instance by putting the necessary code in the
.Rprofile file. This object needs to be a named list of schemes, and
it will be collected when the Givz package loads. Its content is then
automatically added to the collection of available schemes.
Please note that because display parameters are stored with the track objects, a scheme change only has an effect on those objects that are created after the change has taken place.
Value
The getScheme function returns current scheme as a list structure.
Display Parameters
- GenomeAxisTrack:
-
add35=FALSE:Logical scalar. Add 3' to 5' direction indicators.
add53=FALSE:Logical scalar. Add 5' to 3' direction indicators.
background.title="transparent":Character scalar. The background color for the title panel. Defaults to omit the background.
cex.id=0.7:Numeric scalar. The text size for the optional range annotation.
cex=0.8:Numeric scalar. The overall font expansion factor for the axis annotation text.
col.border.title="transparent":Integer or character scalar. The border color for the title panels.
lwd.border.title=1:Integer scalar. The border width for the title panels.
col.id="white":Character scalar. The text color for the optional range annotation.
col.range="cornsilk4":Character scalar. The border color for highlighted regions on the axis.
distFromAxis=1:Numeric scalar. Control the distance of the axis annotation from the tick marks.
exponent=NULL:Numeric scalar. The exponent for the axis coordinates, e.g., 3 means mb, 6 means gb, etc. The default is to automatically determine the optimal exponent.
fill.range="cornsilk3":Character scalar. The fill color for highlighted regions on the axis.
fontcolor="#808080":Character scalar. The font color for the axis annotation text.
fontsize=10:Numeric scalar. Font size for the axis annotation text in points.
labelPos="alternating":Character vector, one in "alternating", "revAlternating", "above" or "below". The vertical positioning of the axis labels. If
scaleis notNULL, the possible values are "above", "below" and "beside".littleTicks=FALSE:Logical scalar. Add more fine-grained tick marks.
lwd=2:Numeric scalar. The line width for the axis elementes.
scale=NULL:Numeric scalar. If not
NULLa small scale is drawn instead of the full axis, if the value is between 0 and 1 it is interpreted as a fraction of the current plotting region, otherwise as an absolute length value in genomic coordinates.showId=FALSE:Logical scalar. Show the optional range highlighting annotation.
showTitle=FALSE:Logical scalar. Plot a title panel. Defaults to omit the title panel.
ticksAt=NULL:Numeric scalar. The exact x-position for tickmarks (in base-pairs).
size=NULL:Numeric scalar. The relative size of the track. Can be overridden in the
plotTracksfunction. Defaults to the ideal size based on the other track settings.col="darkgray":Character scalar. The color for the axis lines and tickmarks.
Inherited from class GdObject:
alpha=1:Numeric scalar. The transparency for all track items.
alpha.title=NULL:Numeric scalar. The transparency for the title panel.
background.panel="transparent":Integer or character scalar. The background color of the content panel.
background.legend="transparent":Integer or character scalar. The background color for the legend.
cex.axis=NULL:Numeric scalar. The expansion factor for the axis annotation. Defaults to
NULL, in which case it is automatically determined based on the available space.cex.title=NULL:Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults to
NULL, which means that the text size is automatically adjusted to the available space.col.axis="white":Integer or character scalar. The font and line color for the y axis, if any.
col.frame="lightgray":Integer or character scalar. The line color used for the panel frame, if
frame==TRUEcol.grid="#808080":Integer or character scalar. Default line color for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.col.line=NULL:Integer or character scalar. Default colors for plot lines. Usually the same as the global
colparameter.col.symbol=NULL:Integer or character scalar. Default colors for plot symbols. Usually the same as the global
colparameter.col.title="white":Integer or character scalar. The border color for the title panels
collapse=TRUE:Boolean controlling whether to collapse the content of the track to accomodate the minimum current device resolution. See
collapsingfor details.fill="lightgray":Integer or character scalar. Default fill color setting for all plotting elements, unless there is a more specific control defined elsewhere.
fontface.title=2:Integer or character scalar. The font face for the title panels.
fontface=1:Integer or character scalar. The font face for all text, unless a more specific definition exists.
fontfamily.title="sans":Integer or character scalar. The font family for the title panels.
fontfamily="sans":Integer or character scalar. The font family for all text, unless a more specific definition exists.
frame=FALSE:Boolean. Draw a frame around the track when plotting.
grid=FALSE:Boolean, switching on/off the plotting of a grid.
h=-1:Integer scalar. Parameter controlling the number of horizontal grid lines, see
panel.gridfor details.lineheight=1:Numeric scalar. The font line height for all text, unless a more specific definition exists.
lty.grid="solid":Integer or character scalar. Default line type for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.lty="solid":Numeric scalar. Default line type setting for all plotting elements, unless there is a more specific control defined elsewhere.
lwd.title=1:Integer scalar. The border width for the title panels
lwd.grid=1:Numeric scalar. Default line width for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.min.distance=1:Numeric scalar. The minimum pixel distance before collapsing range items, only if
collapse==TRUE. Seecollapsingfor details.min.height=3:Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.min.width=1:Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.reverseStrand=FALSE:Logical scalar. Set up the plotting coordinates in 3' -> 5' direction if
TRUE. This will effectively mirror the plot on the vertical axis.rotation.title=90:The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.
rotation=0:The rotation angle for all text unless a more specific definiton exists.
showAxis=TRUE:Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).
v=-1:Integer scalar. Parameter controlling the number of vertical grid lines, see
panel.gridfor details.
- DataTrack:
-
aggregateGroups=FALSE:Logical scalar. Aggregate the values within a sample group using the aggregation funnction specified in the
aggregationparameter.aggregation="mean":Function or character scalar. Used to aggregate values in windows or for collapsing overlapping items. The function has to accept a numeric vector as a single input parameter and has to return a numeric scalar with the aggregated value. Alternatively, one of the predefined options
mean,mediansum,min,maxorextremecan be supplied as a character scalar. Defaults tomean.missingAsZero=TRUE:Logical scalar. Defines how the missing values are treated in the aggregation procedure with running window. Setting it to
TRUEfills empty positions with zeros, which is default.FALSEfills empty positions withNA.alpha.confint=0.3:Numeric scalar. The transparency for the confidence intervalls in confint-type plots.
amount=NULL:Numeric scalar. Amount of jittering in xy-type plots. See
panel.xyplotfor details.baseline=NULL:Numeric scalar. Y-axis position of an optional baseline. This parameter has a special meaning for mountain-type and polygon-type plots, see the 'Details' section in
DataTrackfor more information.box.legend=FALSE:Logical scalar. Draw a box around a legend.
box.ratio=1:Numeric scalar. Parameter controlling the boxplot appearance. See
panel.bwplotfor details.box.width=NULL:Numeric scalar. Parameter controlling the boxplot appearance. See
panel.bwplotfor details.grid=FALSE:Logical vector. Draw a line grid under the track content.
cex.legend=0.8:Numeric scalar. The size factor for the legend text.
cex.sampleNames=NULL:Numeric scalar. The size factor for the sample names text in heatmap or horizon plots. Defaults to an automatic setting.
cex=0.7:Numeric scalar. The default pixel size for plotting symbols.
coef=1.5:Numeric scalar. Parameter controlling the boxplot appearance. See
panel.bwplotfor details.col.baseline=NULL:Character scalar. Color for the optional baseline, defaults to the setting of
col.col.confint=NA:Character vector. Border colors for the confidence intervals for confint-type plots.
col.boxplotFrame="#808080":Character scalar. Line color of the frame around grouped boxplots.
col.histogram="#808080":Character scalar. Line color in histogram-type plots.
col.horizon=NA:The line color for the segments in the
horizon-type plot. Seehorizonplotfor details.col.mountain=NULL:Character scalar. Line color in mountain-type and polygon-type plots, defaults to the setting of
col.col.sampleNames="white":Character or integer scalar. The color used for the sample names in heatmap plots.
col=c("#0080ff", "#ff00ff", "darkgreen", "#ff0000", "orange", "#00ff00", "brown"):Character or integer vector. The color used for all line and symbol elements, unless there is a more specific control defined elsewhere. Unless
groupsare specified, only the first color in the vector is usually regarded.collapse=FALSE:Logical scalar. Collapse overlapping ranges and aggregate the underlying data.
degree=1:Numeric scalar. Parameter controlling the loess calculation for smooth and mountain-type plots. See
panel.loessfor details.do.out=TRUE:Logical scalar. Parameter controlling the boxplot appearance. See
panel.bwplotfor details.evaluation=50:Numeric scalar. Parameter controlling the loess calculation for smooth and mountain-type plots. See
panel.loessfor details.factor=0.5:Numeric scalar. Factor to control amount of jittering in xy-type plots. See
panel.xyplotfor details.family="symmetric":Character scalar. Parameter controlling the loess calculation for smooth and mountain-type plots. See
panel.loessfor details.fill.confint=NULL:Character vector. Fill colors for the confidence intervals for confint-type plots.
fill.histogram=NULL:Character scalar. Fill color in histogram-type plots, defaults to the setting of
fill.fill.horizon=c("#B41414", "#E03231", "#F7A99C", "#9FC8DC", "#468CC8", "#0165B3"):The fill colors for the segments in the
horizon-type plot. This should be a vector of length six, where the first three entries are the colors for positive changes, and the latter three entries are the colors for negative changes. Defaults to a red-blue color scheme. Seehorizonplotfor details.fill.mountain=c("#CCFFFF", "#FFCCFF"):Character vector of length 2. Fill color in mountain-type and polygon-type plots.
fontface.legend=NULL:Integer or character scalar. The font face for the legend text.
fontfamily.legend=NULL:Integer or character scalar. The font family for the legend text.
fontsize.legend=NULL:Numeric scalar. The pixel size for the legend text.
fontcolor.legend="#808080":Integer or character scalar. The font color for the legend text.
gradient=c("#F7FBFF", "#DEEBF7", "#C6DBEF", "#9ECAE1", "#6BAED6", "#4292C6", "#2171B5", "#08519C", "#08306B"):Character vector. The base colors for the
gradientplotting type or theheatmaptype with a single group. When plotting heatmaps with more than one group, thecolparameter can be used to control the group color scheme, however the gradient will always be from white to 'col' and thus does not offer as much flexibility as thisgradientparameter.groups=NULL:Vector coercable to a factor. Optional sample grouping. See 'Details' section in
DataTrackfor further information.horizon.origin=0:The baseline relative to which changes are indicated on the
horizon-type plot. Seehorizonplotfor details.horizon.scale=NULL:The scale for each of the segments in the
horizon-type plot. Defaults to 1/3 of the absolute data range. Seehorizonplotfor details.jitter.x=FALSE:Logical scalar. Toggle on jittering on the x axis in xy-type plots. See
panel.xyplotfor details.jitter.y=FALSE:Logical scalar. Toggle off jittering on the y axis in xy-type plots. See
panel.xyplotfor details.levels.fos=NULL:Numeric scalar. Parameter controlling the boxplot appearance. See
panel.bwplotfor details.legend=TRUE:Boolean triggering the addition of a legend to the track to indicate groups. This only has an effect if at least two groups are present.
lineheight.legend=NULL:Numeric scalar. The line height for the legend text.
lty.baseline=NULL:Character or numeric scalar. Line type of the optional baseline, defaults to the setting of
lty.lty.mountain=NULL:Character or numeric scalar. Line type in mountain-type and polygon-type plots, defaults to the setting of
lty.lwd.baseline=NULL:Numeric scalar. Line width of the optional baseline, defaults to the setting of
lwd.lwd.mountain=NULL:Numeric scalar. Line width in mountain-type and polygon-type plots, defaults to the setting of
lwd.min.distance=0:Numeric scalar. The mimimum distance in pixel below which to collapse ranges.
na.rm=FALSE:Boolean controlling whether to discard all NA values when plotting or to keep empty spaces for NAs
ncolor=100:Integer scalar. The number of colors for the 'gradient' plotting type
notch.frac=0.5:Numeric scalar. Parameter controlling the boxplot appearance. See
panel.bwplotfor details.notch=FALSE:Logical scalar. Parameter controlling the boxplot appearance. See
panel.bwplotfor details.pch=20:Integer scalar. The type of glyph used for plotting symbols.
separator=0:Numeric scalar. Number of pixels used to separate individual samples in heatmap- and horizon-type plots.
showColorBar=TRUE:Boolean. Indicate the data range color mapping in the axis for 'heatmap' or 'gradient' types.
showSampleNames=FALSE:Boolean. Display the names of the individual samples in a heatmap or a horizon plot.
size=NULL:Numeric scalar. The relative size of the track. Can be overridden in the
plotTracksfunction. By default the size will be set automatically based on the selected plotting type.span=0.2:Numeric scalar. Parameter controlling the loess calculation for smooth and mountain-type plots. See
panel.loessfor details.stackedBars=TRUE:Logical scalar. When there are several data groups, draw the histogram-type plots as stacked barplots or grouped side by side.
stats=X[[i]]:Function. Parameter controlling the boxplot appearance. See
panel.bwplotfor details.transformation=NULL:Function. Applied to the data matrix prior to plotting or when calling the
scoremethod. The function should accept exactly one input argument and its return value needs to be a numeric vector which can be coerced back into a data matrix of identical dimensionality as the input data.type="p":Character vector. The plot type, one or several in
p,l,b,a,a_confint,s,g,r,S,confint,smooth,histogram,mountain,polygon,h,boxplot,gradient,heatmap,horizon. See 'Details' section inDataTrackfor more information on the individual plotting types.varwidth=FALSE:Logical scalar. Parameter controlling the boxplot appearance. See
panel.bwplotfor details.window=NULL:Numeric or character scalar. Aggregate the rows values of the data matrix to
windowequally sized slices on the data range using the method defined inaggregation. If negative, apply a running window of sizewindowSizeusing the same aggregation method. Alternatively, the special valueautocauses the function to determine the optimal window size to avoid overplotting, andfixeduses fixed-size windows of sizewindowSize.windowSize=NULL:Numeric scalar. The size of the running window when the value of
windowis negative.ylim=NULL:Numeric vector of length 2. The range of the y-axis scale.
yTicksAt=NULL:Numeric vector. The points at which y-axis tick-marks are to be drawn. By default, when
NULL, tickmark locations are computed.
Inherited from class GdObject:
alpha=1:Numeric scalar. The transparency for all track items.
alpha.title=NULL:Numeric scalar. The transparency for the title panel.
background.panel="transparent":Integer or character scalar. The background color of the content panel.
background.title="lightgray":Integer or character scalar. The background color for the title panel.
background.legend="transparent":Integer or character scalar. The background color for the legend.
cex.axis=NULL:Numeric scalar. The expansion factor for the axis annotation. Defaults to
NULL, in which case it is automatically determined based on the available space.cex.title=NULL:Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults to
NULL, which means that the text size is automatically adjusted to the available space.col.axis="white":Integer or character scalar. The font and line color for the y axis, if any.
col.border.title="white":Integer or character scalar. The border color for the title panels.
col.frame="lightgray":Integer or character scalar. The line color used for the panel frame, if
frame==TRUEcol.grid="#808080":Integer or character scalar. Default line color for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.col.line=NULL:Integer or character scalar. Default colors for plot lines. Usually the same as the global
colparameter.col.symbol=NULL:Integer or character scalar. Default colors for plot symbols. Usually the same as the global
colparameter.col.title="white":Integer or character scalar. The border color for the title panels
fill="lightgray":Integer or character scalar. Default fill color setting for all plotting elements, unless there is a more specific control defined elsewhere.
fontcolor="black":Integer or character scalar. The font color for all text, unless a more specific definition exists.
fontface.title=2:Integer or character scalar. The font face for the title panels.
fontface=1:Integer or character scalar. The font face for all text, unless a more specific definition exists.
fontfamily.title="sans":Integer or character scalar. The font family for the title panels.
fontfamily="sans":Integer or character scalar. The font family for all text, unless a more specific definition exists.
fontsize=12:Numeric scalar. The font size for all text, unless a more specific definition exists.
frame=FALSE:Boolean. Draw a frame around the track when plotting.
h=-1:Integer scalar. Parameter controlling the number of horizontal grid lines, see
panel.gridfor details.lineheight=1:Numeric scalar. The font line height for all text, unless a more specific definition exists.
lty.grid="solid":Integer or character scalar. Default line type for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.lty="solid":Numeric scalar. Default line type setting for all plotting elements, unless there is a more specific control defined elsewhere.
lwd.border.title=1:Integer scalar. The border width for the title panels.
lwd.title=1:Integer scalar. The border width for the title panels
lwd.grid=1:Numeric scalar. Default line width for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.lwd=1:Numeric scalar. Default line width setting for all plotting elements, unless there is a more specific control defined elsewhere.
min.height=3:Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.min.width=1:Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.reverseStrand=FALSE:Logical scalar. Set up the plotting coordinates in 3' -> 5' direction if
TRUE. This will effectively mirror the plot on the vertical axis.rotation.title=90:The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.
rotation=0:The rotation angle for all text unless a more specific definiton exists.
showAxis=TRUE:Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).
showTitle=TRUE:Boolean controlling whether to plot a title panel. Although this can be set individually for each track, in multi-track plots as created by
plotTracksthere will still be an empty placeholder in case any of the other tracks include a title. The same holds true for axes. Note that the the title panel background color could be set to transparent in order to completely hide it.v=-1:Integer scalar. Parameter controlling the number of vertical grid lines, see
panel.gridfor details.
- IdeogramTrack:
-
background.title="transparent":Character scalar. The background color for the title panel. Defaults to omit the background.
bevel=0.45:Numeric scalar, between 0 and 1. The level of smoothness for the two ends of the ideogram.
centromereShape="triangle":Character scalar. The shape of the centromere. Only "triangle" or "circle" is accepted. Default to "triangle"
cex.bands=0.7:Numeric scalar. The font expansion factor for the chromosome band identifier text.
cex=0.8:Numeric scalar. The overall font expansion factor for the chromosome name text.
col="red":Character scalar. The border color used for the highlighting of the currently displayed genomic region.
col.border.title="transparent":Integer or character scalar. The border color for the title panels.
lwd.border.title=1:Integer scalar. The border width for the title panels.
fill="#FFE3E6":Character scalar. The fill color used for the highlighting of the currently displayed genomic region.
fontface=1:Character scalar. The font face for the chromosome name text.
fontfamily="sans":Character scalar. The font family for the chromosome name text.
fontcolor="#808080":Character scalar. The font color for the chromosome name text.
fontsize=10:Numeric scalar. The font size for the chromosome name text.
outline=FALSE:Logical scalar. Add borders to the individual chromosome staining bands.
showBandId=FALSE:Logical scalar. Show the identifier for the chromosome bands if there is space for it.
lty=1:Character or integer scalar. The line type used for the highlighting of the currently displayed genomic region.
lwd=1:Numeric scalar. The line width used for the highlighting of the currently displayed genomic region.
showId=TRUE:Logical scalar. Indicate the chromosome name next to the ideogram.
showTitle=FALSE:Logical scalar. Plot a title panel. Defaults to omit the title panel.
size=NULL:Numeric scalar. The relative size of the track. Defaults to automatic size setting. Can also be overridden in the
plotTracksfunction.
Inherited from class GdObject:
alpha=1:Numeric scalar. The transparency for all track items.
alpha.title=NULL:Numeric scalar. The transparency for the title panel.
background.panel="transparent":Integer or character scalar. The background color of the content panel.
background.legend="transparent":Integer or character scalar. The background color for the legend.
cex.axis=NULL:Numeric scalar. The expansion factor for the axis annotation. Defaults to
NULL, in which case it is automatically determined based on the available space.cex.title=NULL:Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults to
NULL, which means that the text size is automatically adjusted to the available space.col.axis="white":Integer or character scalar. The font and line color for the y axis, if any.
col.frame="lightgray":Integer or character scalar. The line color used for the panel frame, if
frame==TRUEcol.grid="#808080":Integer or character scalar. Default line color for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.col.line=NULL:Integer or character scalar. Default colors for plot lines. Usually the same as the global
colparameter.col.symbol=NULL:Integer or character scalar. Default colors for plot symbols. Usually the same as the global
colparameter.col.title="white":Integer or character scalar. The border color for the title panels
collapse=TRUE:Boolean controlling whether to collapse the content of the track to accomodate the minimum current device resolution. See
collapsingfor details.fontface.title=2:Integer or character scalar. The font face for the title panels.
fontfamily.title="sans":Integer or character scalar. The font family for the title panels.
frame=FALSE:Boolean. Draw a frame around the track when plotting.
grid=FALSE:Boolean, switching on/off the plotting of a grid.
h=-1:Integer scalar. Parameter controlling the number of horizontal grid lines, see
panel.gridfor details.lineheight=1:Numeric scalar. The font line height for all text, unless a more specific definition exists.
lty.grid="solid":Integer or character scalar. Default line type for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.lwd.title=1:Integer scalar. The border width for the title panels
lwd.grid=1:Numeric scalar. Default line width for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.min.distance=1:Numeric scalar. The minimum pixel distance before collapsing range items, only if
collapse==TRUE. Seecollapsingfor details.min.height=3:Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.min.width=1:Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.reverseStrand=FALSE:Logical scalar. Set up the plotting coordinates in 3' -> 5' direction if
TRUE. This will effectively mirror the plot on the vertical axis.rotation.title=90:The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.
rotation=0:The rotation angle for all text unless a more specific definiton exists.
showAxis=TRUE:Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).
v=-1:Integer scalar. Parameter controlling the number of vertical grid lines, see
panel.gridfor details.
- AnnotationTrack:
-
arrowHeadWidth=30:Numeric scalar. The width of the arrow head in pixels if
shapeisfixedArrow.arrowHeadMaxWidth=40:Numeric scalar. The maximum width of the arrow head in pixels if
shapeisarrow.cex.group=0.6:Numeric scalar. The font expansion factor for the group-level annotation.
cex=1:Numeric scalar. The font expansion factor for item identifiers.
col.line="darkgray":Character scalar. The color used for connecting lines between grouped items. Defaults to a light gray, but if set to
NULLthe same color as for the first item in the group is used.col="transparent":Character or integer scalar. The border color for all track items.
featureAnnotation=NULL:Character scalar. Add annotation information to the individual track elements. This can be a value in
id,grouporfeature. Defaults toid. Only works ifshowFeatureIdis notFALSE.fill="lightblue":Character or integer scalar. The fill color for untyped items. This is also used to connect grouped items. See
groupingfor details.fontfamily.group="sans":Character scalar. The font family for the group-level annotation.
fontcolor.group="#808080":Character or integer scalar. The font color for the group-level annotation.
fontcolor.item="white":Character or integer scalar. The font color for item identifiers.
fontface.group=2:Numeric scalar. The font face for the group-level annotation.
fontsize.group=12:Numeric scalar. The font size for the group-level annotation.
groupAnnotation=NULL:Character scalar. Add annotation information as group labels. This can be a value in
id,grouporfeature. Defaults togroup. Only works ifshowIdis notFALSE.just.group="left":Character scalar. the justification of group labels. Either
left,right,aboveorbelow.lex=1:Numeric scalar. The line expansion factor for all track items. This is also used to connect grouped items. See
groupingfor details.lineheight=1:Numeric scalar. The font line height for item identifiers.
lty="solid":Character or integer scalar. The line type for all track items. This is also used to connect grouped items. See
groupingfor details.lwd=1:Integer scalar. The line width for all track items. This is also used to connect grouped items. See
groupingfor details.mergeGroups=FALSE:Logical scalar. Merge fully overlapping groups if
collapse==TRUE.min.height=3:Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details. For feathered bars indicating the strandedness of grouped items this also controls the height of the arrow feathers.min.width=1:Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.rotation=0:Numeric scalar. The degree of text rotation for item identifiers.
rotation.group=0:Numeric scalar. The degree of text rotation for group labels.
rotation.item=0:Numeric scalar. The degree of text rotation for item identifiers.
shape="arrow":Character scalar. The shape in which to display the track items. Currently only
box,arrow,fixedArrow,ellipse, andsmallArroware implemented.showFeatureId=FALSE:Logical scalar. Control whether to plot the individual track item identifiers.
showId=FALSE:Logical scalar. Control whether to annotate individual groups.
showOverplotting=FALSE:Logical scalar. Use a color gradient to show the amount of overplotting for collapsed items. This implies that
collapse==TRUEsize=1:Numeric scalar. The relative size of the track. Can be overridden in the
plotTracksfunction.
Inherited from class StackedTrack:
stackHeight=0.75:Numeric between 0 and 1. Controls the vertical size and spacing between stacked elements. The number defines the proportion of the total available space for the stack that is used to draw the glyphs. E.g., a value of 0.5 means that half of the available vertical drawing space (for each stacking line) is used for the glyphs, and thus one quarter of the available space each is used for spacing above and below the glyph. Defaults to 0.75.
reverseStacking=FALSE:Logical flag. Reverse the y-ordering of stacked items. I.e., features that are plotted on the bottom-most stacks will be moved to the top-most stack and vice versa.
Inherited from class GdObject:
alpha=1:Numeric scalar. The transparency for all track items.
alpha.title=NULL:Numeric scalar. The transparency for the title panel.
background.panel="transparent":Integer or character scalar. The background color of the content panel.
background.title="lightgray":Integer or character scalar. The background color for the title panel.
background.legend="transparent":Integer or character scalar. The background color for the legend.
cex.axis=NULL:Numeric scalar. The expansion factor for the axis annotation. Defaults to
NULL, in which case it is automatically determined based on the available space.cex.title=NULL:Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults to
NULL, which means that the text size is automatically adjusted to the available space.col.axis="white":Integer or character scalar. The font and line color for the y axis, if any.
col.border.title="white":Integer or character scalar. The border color for the title panels.
col.frame="lightgray":Integer or character scalar. The line color used for the panel frame, if
frame==TRUEcol.grid="#808080":Integer or character scalar. Default line color for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.col.symbol=NULL:Integer or character scalar. Default colors for plot symbols. Usually the same as the global
colparameter.col.title="white":Integer or character scalar. The border color for the title panels
collapse=TRUE:Boolean controlling whether to collapse the content of the track to accomodate the minimum current device resolution. See
collapsingfor details.fontcolor="black":Integer or character scalar. The font color for all text, unless a more specific definition exists.
fontface.title=2:Integer or character scalar. The font face for the title panels.
fontface=1:Integer or character scalar. The font face for all text, unless a more specific definition exists.
fontfamily.title="sans":Integer or character scalar. The font family for the title panels.
fontfamily="sans":Integer or character scalar. The font family for all text, unless a more specific definition exists.
fontsize=12:Numeric scalar. The font size for all text, unless a more specific definition exists.
frame=FALSE:Boolean. Draw a frame around the track when plotting.
grid=FALSE:Boolean, switching on/off the plotting of a grid.
h=-1:Integer scalar. Parameter controlling the number of horizontal grid lines, see
panel.gridfor details.lty.grid="solid":Integer or character scalar. Default line type for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.lwd.border.title=1:Integer scalar. The border width for the title panels.
lwd.title=1:Integer scalar. The border width for the title panels
lwd.grid=1:Numeric scalar. Default line width for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.min.distance=1:Numeric scalar. The minimum pixel distance before collapsing range items, only if
collapse==TRUE. Seecollapsingfor details.reverseStrand=FALSE:Logical scalar. Set up the plotting coordinates in 3' -> 5' direction if
TRUE. This will effectively mirror the plot on the vertical axis.rotation.title=90:The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.
showAxis=TRUE:Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).
showTitle=TRUE:Boolean controlling whether to plot a title panel. Although this can be set individually for each track, in multi-track plots as created by
plotTracksthere will still be an empty placeholder in case any of the other tracks include a title. The same holds true for axes. Note that the the title panel background color could be set to transparent in order to completely hide it.v=-1:Integer scalar. Parameter controlling the number of vertical grid lines, see
panel.gridfor details.
- GeneRegionTrack:
-
arrowHeadWidth=10:Numeric scalar. The width of the arrow head in pixels if
shapeisfixedArrow.arrowHeadMaxWidth=20:Numeric scalar. The maximum width of the arrow head in pixels if
shapeisarrow.col=NULL:Character or integer scalar. The border color for all track items. Defaults to using the same color as in
fill, also taking into account different trackfeatures.collapseTranscripts=FALSE:Logical or character scalar. Can be one in
gene,longest,shortestormeta. Merge all transcripts of the same gene into one single gene model. In the case ofgene(orTRUE), this will only keep the start location of the first exon and the end location of the last exon from all transcripts of the gene. Forshortestandlongest, only the longest or shortest transcript model is retained. Formeta, a meta-transcript containing the union of all exons is formed (essentially identical to the operationreduce(geneModel)).exonAnnotation=NULL:Character scalar. Add annotation information to the individual exon models. This can be a value in
symbol,gene,transcript,exonorfeature. Defaults toexon. Only works ifshowExonIdis notFALSE.fill="orange":Character or integer scalar. The fill color for untyped items. This is also used to connect grouped items. See
groupingfor details.min.distance=0:Numeric scalar. The minimum pixel distance before collapsing range items, only if
collapse==TRUE. Seecollapsingfor details. Note that a value larger than 0 may lead to UTR regions being merged to CDS regions, which in most cases is not particularly useful.shape=c("smallArrow", "box"):Character scalar. The shape in which to display the track items. Currently only
box,arrow,ellipse, andsmallArroware implemented.showExonId=NULL:Logical scalar. Control whether to plot the individual exon identifiers.
thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5", "3UTR", "5UTR", "miRNA", "lincRNA", "three_prime_UTR", "five_prime_UTR"):Character vector. A listing of feature types that should be drawn with thin boxes. Typically those are non-coding elements.
transcriptAnnotation=NULL:Character scalar. Add annotation information as transcript labels. This can be a value in
symbol,gene,transcript,exonorfeature. Defaults tosymbol. Only works ifshowIdis notFALSE.
Inherited from class AnnotationTrack:
cex.group=0.6:Numeric scalar. The font expansion factor for the group-level annotation.
cex=1:Numeric scalar. The font expansion factor for item identifiers.
col.line="darkgray":Character scalar. The color used for connecting lines between grouped items. Defaults to a light gray, but if set to
NULLthe same color as for the first item in the group is used.featureAnnotation=NULL:Character scalar. Add annotation information to the individual track elements. This can be a value in
id,grouporfeature. Defaults toid. Only works ifshowFeatureIdis notFALSE.fontfamily.group="sans":Character scalar. The font family for the group-level annotation.
fontcolor.group="#808080":Character or integer scalar. The font color for the group-level annotation.
fontcolor.item="white":Character or integer scalar. The font color for item identifiers.
fontface.group=2:Numeric scalar. The font face for the group-level annotation.
fontsize.group=12:Numeric scalar. The font size for the group-level annotation.
groupAnnotation=NULL:Character scalar. Add annotation information as group labels. This can be a value in
id,grouporfeature. Defaults togroup. Only works ifshowIdis notFALSE.just.group="left":Character scalar. the justification of group labels. Either
left,right,aboveorbelow.lex=1:Numeric scalar. The line expansion factor for all track items. This is also used to connect grouped items. See
groupingfor details.lineheight=1:Numeric scalar. The font line height for item identifiers.
lty="solid":Character or integer scalar. The line type for all track items. This is also used to connect grouped items. See
groupingfor details.lwd=1:Integer scalar. The line width for all track items. This is also used to connect grouped items. See
groupingfor details.mergeGroups=FALSE:Logical scalar. Merge fully overlapping groups if
collapse==TRUE.min.height=3:Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details. For feathered bars indicating the strandedness of grouped items this also controls the height of the arrow feathers.min.width=1:Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.rotation=0:Numeric scalar. The degree of text rotation for item identifiers.
rotation.group=0:Numeric scalar. The degree of text rotation for group labels.
rotation.item=0:Numeric scalar. The degree of text rotation for item identifiers.
showFeatureId=FALSE:Logical scalar. Control whether to plot the individual track item identifiers.
showId=FALSE:Logical scalar. Control whether to annotate individual groups.
showOverplotting=FALSE:Logical scalar. Use a color gradient to show the amount of overplotting for collapsed items. This implies that
collapse==TRUEsize=1:Numeric scalar. The relative size of the track. Can be overridden in the
plotTracksfunction.
Inherited from class StackedTrack:
stackHeight=0.75:Numeric between 0 and 1. Controls the vertical size and spacing between stacked elements. The number defines the proportion of the total available space for the stack that is used to draw the glyphs. E.g., a value of 0.5 means that half of the available vertical drawing space (for each stacking line) is used for the glyphs, and thus one quarter of the available space each is used for spacing above and below the glyph. Defaults to 0.75.
reverseStacking=FALSE:Logical flag. Reverse the y-ordering of stacked items. I.e., features that are plotted on the bottom-most stacks will be moved to the top-most stack and vice versa.
Inherited from class GdObject:
alpha=1:Numeric scalar. The transparency for all track items.
alpha.title=NULL:Numeric scalar. The transparency for the title panel.
background.panel="transparent":Integer or character scalar. The background color of the content panel.
background.title="lightgray":Integer or character scalar. The background color for the title panel.
background.legend="transparent":Integer or character scalar. The background color for the legend.
cex.axis=NULL:Numeric scalar. The expansion factor for the axis annotation. Defaults to
NULL, in which case it is automatically determined based on the available space.cex.title=NULL:Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults to
NULL, which means that the text size is automatically adjusted to the available space.col.axis="white":Integer or character scalar. The font and line color for the y axis, if any.
col.border.title="white":Integer or character scalar. The border color for the title panels.
col.frame="lightgray":Integer or character scalar. The line color used for the panel frame, if
frame==TRUEcol.grid="#808080":Integer or character scalar. Default line color for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.col.symbol=NULL:Integer or character scalar. Default colors for plot symbols. Usually the same as the global
colparameter.col.title="white":Integer or character scalar. The border color for the title panels
collapse=TRUE:Boolean controlling whether to collapse the content of the track to accomodate the minimum current device resolution. See
collapsingfor details.fontcolor="black":Integer or character scalar. The font color for all text, unless a more specific definition exists.
fontface.title=2:Integer or character scalar. The font face for the title panels.
fontface=1:Integer or character scalar. The font face for all text, unless a more specific definition exists.
fontfamily.title="sans":Integer or character scalar. The font family for the title panels.
fontfamily="sans":Integer or character scalar. The font family for all text, unless a more specific definition exists.
fontsize=12:Numeric scalar. The font size for all text, unless a more specific definition exists.
frame=FALSE:Boolean. Draw a frame around the track when plotting.
grid=FALSE:Boolean, switching on/off the plotting of a grid.
h=-1:Integer scalar. Parameter controlling the number of horizontal grid lines, see
panel.gridfor details.lty.grid="solid":Integer or character scalar. Default line type for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.lwd.border.title=1:Integer scalar. The border width for the title panels.
lwd.title=1:Integer scalar. The border width for the title panels
lwd.grid=1:Numeric scalar. Default line width for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.reverseStrand=FALSE:Logical scalar. Set up the plotting coordinates in 3' -> 5' direction if
TRUE. This will effectively mirror the plot on the vertical axis.rotation.title=90:The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.
showAxis=TRUE:Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).
showTitle=TRUE:Boolean controlling whether to plot a title panel. Although this can be set individually for each track, in multi-track plots as created by
plotTracksthere will still be an empty placeholder in case any of the other tracks include a title. The same holds true for axes. Note that the the title panel background color could be set to transparent in order to completely hide it.v=-1:Integer scalar. Parameter controlling the number of vertical grid lines, see
panel.gridfor details.
- BiomartGeneRegionTrack:
-
C_segment="burlywood4":Character or integer scalar. Fill color for annotation objects of type 'C_segment'.
D_segment="lightblue":Character or integer scalar. Fill color for annotation objects of type 'C_segment'.
J_segment="dodgerblue2":Character or integer scalar. Fill color for annotation objects of type 'C_segment'.
Mt_rRNA="yellow":Character or integer scalar. Fill color for annotation objects of type 'Mt_rRNA'.
Mt_tRNA="darkgoldenrod":Character or integer scalar. Fill color for annotation objects of type 'Mt_tRNA'.
Mt_tRNA_pseudogene="darkgoldenrod1":Character or integer scalar. Fill color for annotation objects of type 'Mt_tRNA_pseudogene'.
V_segment="aquamarine":Character or integer scalar. Fill color for annotation objects of type 'V_segment'.
miRNA="cornflowerblue":Character or integer scalar. Fill color for annotation objects of type 'L_segment'.
miRNA_pseudogene="cornsilk":Character or integer scalar. Fill color for annotation objects of type 'miRNA_pseudogene'.
misc_RNA="cornsilk3":Character or integer scalar. Fill color for annotation objects of type 'misc_RNA'.
misc_RNA_pseudogene="cornsilk4":Character or integer scalar. Fill color for annotation objects of type 'misc_RNA_pseudogene'.
protein_coding="#FFD58A":Character or integer scalar. Fill color for annotation objects of type 'protein_coding'.
pseudogene="brown1":Character or integer scalar. Fill color for annotation objects of type 'pseudogene'.
rRNA="darkolivegreen1":Character or integer scalar. Fill color for annotation objects of type 'rRNA'.
rRNA_pseudogene="darkolivegreen":Character or integer scalar. Fill color for annotation objects of type 'rRNA_pseudogene'.
retrotransposed="blueviolet":Character or integer scalar. Fill color for annotation objects of type 'retrotransposed'.
scRNA="gold4":Character or integer scalar. Fill color for annotation objects of type 'scRNA'.
scRNA_pseudogene="darkorange2":Character or integer scalar. Fill color for annotation objects of type 'scRNA_pseudogene'.
snRNA="coral":Character or integer scalar. Fill color for annotation objects of type 'snRNA'.
snRNA_pseudogene="coral3":Character or integer scalar. Fill color for annotation objects of type 'snRNA_pseudogene'.
snoRNA="cyan":Character or integer scalar. Fill color for annotation objects of type 'snoRNA'.
snoRNA_pseudogene="cyan2":Character or integer scalar. Fill color for annotation objects of type 'snoRNA_pseudogene'.
tRNA_pseudogene="antiquewhite3":Character or integer scalar. Fill color for annotation objects of type 'tRNA_pseudogene'.
utr3="#FFD58A":Character or integer scalar. Fill color for annotation objects of type 'utr3'.
utr5="#FFD58A":Character or integer scalar. Fill color for annotation objects of type 'utr5'.
verbose=FALSE:Logical scalar. Report data loading events from Bioamart or retrieval from cache.
Inherited from class GeneRegionTrack:
arrowHeadWidth=10:Numeric scalar. The width of the arrow head in pixels if
shapeisfixedArrow.arrowHeadMaxWidth=20:Numeric scalar. The maximum width of the arrow head in pixels if
shapeisarrow.col=NULL:Character or integer scalar. The border color for all track items. Defaults to using the same color as in
fill, also taking into account different trackfeatures.collapseTranscripts=FALSE:Logical or character scalar. Can be one in
gene,longest,shortestormeta. Merge all transcripts of the same gene into one single gene model. In the case ofgene(orTRUE), this will only keep the start location of the first exon and the end location of the last exon from all transcripts of the gene. Forshortestandlongest, only the longest or shortest transcript model is retained. Formeta, a meta-transcript containing the union of all exons is formed (essentially identical to the operationreduce(geneModel)).exonAnnotation=NULL:Character scalar. Add annotation information to the individual exon models. This can be a value in
symbol,gene,transcript,exonorfeature. Defaults toexon. Only works ifshowExonIdis notFALSE.fill="orange":Character or integer scalar. The fill color for untyped items. This is also used to connect grouped items. See
groupingfor details.min.distance=0:Numeric scalar. The minimum pixel distance before collapsing range items, only if
collapse==TRUE. Seecollapsingfor details. Note that a value larger than 0 may lead to UTR regions being merged to CDS regions, which in most cases is not particularly useful.shape=c("smallArrow", "box"):Character scalar. The shape in which to display the track items. Currently only
box,arrow,ellipse, andsmallArroware implemented.showExonId=NULL:Logical scalar. Control whether to plot the individual exon identifiers.
thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5", "3UTR", "5UTR", "miRNA", "lincRNA", "three_prime_UTR", "five_prime_UTR"):Character vector. A listing of feature types that should be drawn with thin boxes. Typically those are non-coding elements.
transcriptAnnotation=NULL:Character scalar. Add annotation information as transcript labels. This can be a value in
symbol,gene,transcript,exonorfeature. Defaults tosymbol. Only works ifshowIdis notFALSE.
Inherited from class AnnotationTrack:
cex.group=0.6:Numeric scalar. The font expansion factor for the group-level annotation.
cex=1:Numeric scalar. The font expansion factor for item identifiers.
col.line="darkgray":Character scalar. The color used for connecting lines between grouped items. Defaults to a light gray, but if set to
NULLthe same color as for the first item in the group is used.featureAnnotation=NULL:Character scalar. Add annotation information to the individual track elements. This can be a value in
id,grouporfeature. Defaults toid. Only works ifshowFeatureIdis notFALSE.fontfamily.group="sans":Character scalar. The font family for the group-level annotation.
fontcolor.group="#808080":Character or integer scalar. The font color for the group-level annotation.
fontcolor.item="white":Character or integer scalar. The font color for item identifiers.
fontface.group=2:Numeric scalar. The font face for the group-level annotation.
fontsize.group=12:Numeric scalar. The font size for the group-level annotation.
groupAnnotation=NULL:Character scalar. Add annotation information as group labels. This can be a value in
id,grouporfeature. Defaults togroup. Only works ifshowIdis notFALSE.just.group="left":Character scalar. the justification of group labels. Either
left,right,aboveorbelow.lex=1:Numeric scalar. The line expansion factor for all track items. This is also used to connect grouped items. See
groupingfor details.lineheight=1:Numeric scalar. The font line height for item identifiers.
lty="solid":Character or integer scalar. The line type for all track items. This is also used to connect grouped items. See
groupingfor details.lwd=1:Integer scalar. The line width for all track items. This is also used to connect grouped items. See
groupingfor details.mergeGroups=FALSE:Logical scalar. Merge fully overlapping groups if
collapse==TRUE.min.height=3:Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details. For feathered bars indicating the strandedness of grouped items this also controls the height of the arrow feathers.min.width=1:Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.rotation=0:Numeric scalar. The degree of text rotation for item identifiers.
rotation.group=0:Numeric scalar. The degree of text rotation for group labels.
rotation.item=0:Numeric scalar. The degree of text rotation for item identifiers.
showFeatureId=FALSE:Logical scalar. Control whether to plot the individual track item identifiers.
showId=FALSE:Logical scalar. Control whether to annotate individual groups.
showOverplotting=FALSE:Logical scalar. Use a color gradient to show the amount of overplotting for collapsed items. This implies that
collapse==TRUEsize=1:Numeric scalar. The relative size of the track. Can be overridden in the
plotTracksfunction.
Inherited from class StackedTrack:
stackHeight=0.75:Numeric between 0 and 1. Controls the vertical size and spacing between stacked elements. The number defines the proportion of the total available space for the stack that is used to draw the glyphs. E.g., a value of 0.5 means that half of the available vertical drawing space (for each stacking line) is used for the glyphs, and thus one quarter of the available space each is used for spacing above and below the glyph. Defaults to 0.75.
reverseStacking=FALSE:Logical flag. Reverse the y-ordering of stacked items. I.e., features that are plotted on the bottom-most stacks will be moved to the top-most stack and vice versa.
Inherited from class GdObject:
alpha=1:Numeric scalar. The transparency for all track items.
alpha.title=NULL:Numeric scalar. The transparency for the title panel.
background.panel="transparent":Integer or character scalar. The background color of the content panel.
background.title="lightgray":Integer or character scalar. The background color for the title panel.
background.legend="transparent":Integer or character scalar. The background color for the legend.
cex.axis=NULL:Numeric scalar. The expansion factor for the axis annotation. Defaults to
NULL, in which case it is automatically determined based on the available space.cex.title=NULL:Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults to
NULL, which means that the text size is automatically adjusted to the available space.col.axis="white":Integer or character scalar. The font and line color for the y axis, if any.
col.border.title="white":Integer or character scalar. The border color for the title panels.
col.frame="lightgray":Integer or character scalar. The line color used for the panel frame, if
frame==TRUEcol.grid="#808080":Integer or character scalar. Default line color for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.col.symbol=NULL:Integer or character scalar. Default colors for plot symbols. Usually the same as the global
colparameter.col.title="white":Integer or character scalar. The border color for the title panels
collapse=TRUE:Boolean controlling whether to collapse the content of the track to accomodate the minimum current device resolution. See
collapsingfor details.fontcolor="black":Integer or character scalar. The font color for all text, unless a more specific definition exists.
fontface.title=2:Integer or character scalar. The font face for the title panels.
fontface=1:Integer or character scalar. The font face for all text, unless a more specific definition exists.
fontfamily.title="sans":Integer or character scalar. The font family for the title panels.
fontfamily="sans":Integer or character scalar. The font family for all text, unless a more specific definition exists.
fontsize=12:Numeric scalar. The font size for all text, unless a more specific definition exists.
frame=FALSE:Boolean. Draw a frame around the track when plotting.
grid=FALSE:Boolean, switching on/off the plotting of a grid.
h=-1:Integer scalar. Parameter controlling the number of horizontal grid lines, see
panel.gridfor details.lty.grid="solid":Integer or character scalar. Default line type for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.lwd.border.title=1:Integer scalar. The border width for the title panels.
lwd.title=1:Integer scalar. The border width for the title panels
lwd.grid=1:Numeric scalar. Default line width for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.reverseStrand=FALSE:Logical scalar. Set up the plotting coordinates in 3' -> 5' direction if
TRUE. This will effectively mirror the plot on the vertical axis.rotation.title=90:The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.
showAxis=TRUE:Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).
showTitle=TRUE:Boolean controlling whether to plot a title panel. Although this can be set individually for each track, in multi-track plots as created by
plotTracksthere will still be an empty placeholder in case any of the other tracks include a title. The same holds true for axes. Note that the the title panel background color could be set to transparent in order to completely hide it.v=-1:Integer scalar. Parameter controlling the number of vertical grid lines, see
panel.gridfor details.
- AlignmentsTrack:
-
alpha.reads=0.5:Numeric scalar between 0 and 1. The transparency of the individual read icons. Can be used to indicate overlapping regions in read pairs. Only on supported devices.
alpha.mismatch=1:Numeric scalar between 0 and 1. The transparency of the mismatch base information.
cex=0.7:Numeric Scalar. The global character expansion factor.
cex.mismatch=NULL:Numeric Scalar. The character expansion factor for the mismatch base letters.
col.coverage=NULL:Integer or character scalar. The line color for the coverage profile.
col.gap="#808080":Integer or character scalar. The color of the line that is bridging the gap regions in gapped alignments.
col.mates="#E0E0E0":Integer or character scalar. The color of the line that is connecting two paired reads.
col.deletion="#000000":Integer or character scalar. The color of the line that is bridging the deleted regions in alignments.
col.insertion="#984EA3":Integer or character scalar. The color of the line that highlighting insertions in alignments.
col.mismatch="#808080":Integer or character scalar. The box color around mismatch bases.
col.reads=NULL:Integer or character scalar. The box color around reads.
col.sashimi=NULL:Integer or character scalar. The line color for sashimi plots.
col="#808080":Integer or character scalar. The default color of all line elements.
collapse=FALSE:Logical scalar. Do not perform any collapsing of overlapping elements. Currently not supported.
coverageHeight=0.1:Numeric scalar. The height of the coverage region of the track. Can either be a value between 0 and 1 in which case it is taken as a relative height, or a positive value greater 1 in which case it is interpreted as pixels.
fill.coverage=NULL:Integer or character scalar. The fill color for the coverage profile.
fill.reads=NULL:Integer or character scalar. The fill color for the read icons.
fill="#BABABA":Integer or character scalar. The default fill color of all plot elements.
fontface.mismatch=2:Integer scalar. The font face for mismatch bases.
lty.coverage=NULL:Integer or character scalar. The line type of the coverage profile.
lty.gap=NULL:Integer or character scalar. The type of the line that is bridging the gap regions in gapped alignments.
lty.mates=NULL:Integer or character scalar. The type of the line that is connecting two paired reads.
lty.deletion=NULL:Integer or character scalar. The type of the line that is bridging the deleted regions in alignments.
lty.insertion=NULL:Integer or character scalar. The type of the line that highlighting insertions in alignments.
lty.mismatch=NULL:Integer or character scalar. The box line type around mismatch bases.
lty.reads=NULL:Integer or character scalar. The box line type around mismatch reads.
lty=1:Integer or character scalar. The default type of all line elements.
lwd.coverage=NULL:Integer or character scalar. The line width of the coverage profile.
lwd.gap=NULL:Integer scalar. The width of the line that is bridging the gap regions in gapped alignments.
lwd.mates=NULL:Integer scalar. The width of the line that is connecting two paired reads.
lwd.deletion=NULL:Integer scalar. The width of the line that is bridging the deleted regions in alignments.
lwd.insertion=NULL:Integer scalar. The width of the line that highlighting insertions in alignments.
lwd.mismatch=NULL:Integer scalar. The box line width around mismatch bases.
lwd.reads=NULL:Integer scalar. The box line width around reads.
lwd.sashimiMax=10:Integer scalar. The maximal width of the line in sashimi plots.
lwd=1:Integer scalar. The default width of all line elements.
max.height=10:Integer scalar. The maximum height of an individual read in pixels. Can be used in combination with
min.heightto control the read and stacking appearance.min.height=5:Integer scalar. The minimum height of an individual read in pixels. Can be used in combination with
max.heightto control the read and stacking appearance.minCoverageHeight=50:Integer scalar. The minimum height of the coverage section. Uselful in combination with a relative setting of
coverageHeight.minSashimiHeight=50:Integer scalar. The minimum height of the sashimi section. Uselful in combination with a relative setting of
sashimiHeight.noLetters=FALSE:Logical scalar. Always plot colored boxes for mismatch bases regardles of the available space.
sashimiFilter=NULL:GRanges object. Only junctions which overlap equally with
sashimiFilterGRanges are shown. DefaultNULL, no filtering.sashimiFilterTolerance=0:Integer scalar. Only used in combination with
sashimiFilter. It allows to include junctions whose starts/ends are within specified distance fromsashimiFilterGRanges. This is useful for cases where the aligner did not place the junction reads precisely. Default0L, no tolerance.sashimiHeight=0.1:Integer scalar. The height of the sashimi part of the track. Can either be a value between 0 and 1 in which case it is taken as a relative height, or a positive value greater 1 in which case it is interpreted as pixels.
sashimiScore=1:Integer scalar. The minimum number of reads supporting the junction.
sashimiStrand="*":Integer scalar. Only reads which have the specified strand are considered to count the junctions.
sashimiTransformation=NULL:Function. Applied to the junction score vector prior to plotting. The function should accept exactly one input argument and its return value needs to be a numeric vector of identical length as the input data.
showIndels=FALSE:Logical scalar. Consider insertions and deletions in coverage and pile-up. Default is
FALSE. If set toTRUEthe deletions defined in CIGAR string are not considered in coverage plot. The deletions are displayed as bridging lines in pile-up track. Insertions are shown as vertical bars.showMismatches=TRUE:Logical scalar. Add mismatch information, either as individual base letters or using color coded bars. This implies that the reference sequence has been provided, either to the class constructor or as part of the track list.
size=NULL:Numeric scalar. The size of the track. Defaults to automatic sizing.
transformation=NULL:Function. Applied to the coverage vector prior to plotting. The function should accept exactly one input argument and its return value needs to be a numeric Rle of identical length as the input data.
type=c("coverage", "pileup"):Character vactor. The type of information to plot. For
coveragea coverage plot, potentially augmented by base mismatch information, forsashimia sashimi plot, showing the juctions, and forpileupthe pileups of the individual reads. These three can be combined.
Inherited from class StackedTrack:
stackHeight=0.75:Numeric between 0 and 1. Controls the vertical size and spacing between stacked elements. The number defines the proportion of the total available space for the stack that is used to draw the glyphs. E.g., a value of 0.5 means that half of the available vertical drawing space (for each stacking line) is used for the glyphs, and thus one quarter of the available space each is used for spacing above and below the glyph. Defaults to 0.75.
reverseStacking=FALSE:Logical flag. Reverse the y-ordering of stacked items. I.e., features that are plotted on the bottom-most stacks will be moved to the top-most stack and vice versa.
Inherited from class GdObject:
alpha=1:Numeric scalar. The transparency for all track items.
alpha.title=NULL:Numeric scalar. The transparency for the title panel.
background.panel="transparent":Integer or character scalar. The background color of the content panel.
background.title="lightgray":Integer or character scalar. The background color for the title panel.
background.legend="transparent":Integer or character scalar. The background color for the legend.
cex.axis=NULL:Numeric scalar. The expansion factor for the axis annotation. Defaults to
NULL, in which case it is automatically determined based on the available space.cex.title=NULL:Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults to
NULL, which means that the text size is automatically adjusted to the available space.col.axis="white":Integer or character scalar. The font and line color for the y axis, if any.
col.border.title="white":Integer or character scalar. The border color for the title panels.
col.frame="lightgray":Integer or character scalar. The line color used for the panel frame, if
frame==TRUEcol.grid="#808080":Integer or character scalar. Default line color for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.col.line=NULL:Integer or character scalar. Default colors for plot lines. Usually the same as the global
colparameter.col.symbol=NULL:Integer or character scalar. Default colors for plot symbols. Usually the same as the global
colparameter.col.title="white":Integer or character scalar. The border color for the title panels
fontcolor="black":Integer or character scalar. The font color for all text, unless a more specific definition exists.
fontface.title=2:Integer or character scalar. The font face for the title panels.
fontface=1:Integer or character scalar. The font face for all text, unless a more specific definition exists.
fontfamily.title="sans":Integer or character scalar. The font family for the title panels.
fontfamily="sans":Integer or character scalar. The font family for all text, unless a more specific definition exists.
fontsize=12:Numeric scalar. The font size for all text, unless a more specific definition exists.
frame=FALSE:Boolean. Draw a frame around the track when plotting.
grid=FALSE:Boolean, switching on/off the plotting of a grid.
h=-1:Integer scalar. Parameter controlling the number of horizontal grid lines, see
panel.gridfor details.lineheight=1:Numeric scalar. The font line height for all text, unless a more specific definition exists.
lty.grid="solid":Integer or character scalar. Default line type for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.lwd.border.title=1:Integer scalar. The border width for the title panels.
lwd.title=1:Integer scalar. The border width for the title panels
lwd.grid=1:Numeric scalar. Default line width for grid lines, both when
type=="g"inDataTracks and when display parametergrid==TRUE.min.distance=1:Numeric scalar. The minimum pixel distance before collapsing range items, only if
collapse==TRUE. Seecollapsingfor details.min.width=1:Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See
collapsingfor details.reverseStrand=FALSE:Logical scalar. Set up the plotting coordinates in 3' -> 5' direction if
TRUE. This will effectively mirror the plot on the vertical axis.rotation.title=90:The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.
rotation=0:The rotation angle for all text unless a more specific definiton exists.
showAxis=TRUE:Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).
showTitle=TRUE:Boolean controlling whether to plot a title panel. Although this can be set individually for each track, in multi-track plots as created by
plotTracksthere will still be an empty placeholder in case any of the other tracks include a title. The same holds true for axes. Note that the the title panel background color could be set to transparent in order to completely hide it.v=-1:Integer scalar. Parameter controlling the number of vertical grid lines, see
panel.gridfor details.
Author(s)
Florian Hahne
See Also
AnnotationTrack
DataTrack
DisplayPars
GdObject
availableDisplayPars
collapsing
grouping
horizonplot
panel.bwplot
panel.grid
panel.loess
panel.xyplot
plotTracks
Examples
## Which scheme is used?
getOption("Gviz.scheme")
## Change default settings for GeneRegionTrack
scheme <- getScheme()
scheme$GeneRegionTrack$fill <- "salmon"
scheme$GeneRegionTrack$col <- NULL
scheme$GeneRegionTrack$transcriptAnnotation <- "transcript"
## replace default scheme with myScheme
addScheme(scheme, "myScheme")
options(Gviz.scheme = "myScheme")
getOption("Gviz.scheme")
data(geneModels)
grtrack <- GeneRegionTrack(geneModels, genome = "hg19", chromosome = "chr7", name = "Gene Model")
plotTracks(grtrack)
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