| Type: | Package |
| Title: | Incrementally Build Complex Plots using Natural Semantics |
| Version: | 0.2.0 |
| URL: | https://github.com/zwdzwd/wheatmap |
| BugReports: | https://github.com/zwdzwd/wheatmap/issues |
| Description: | Builds complex plots, heatmaps in particular, using natural semantics. Bigger plots can be assembled using directives such as 'LeftOf', 'RightOf', 'TopOf', and 'Beneath' and more. Other features include clustering, dendrograms and integration with 'ggplot2' generated grid objects. This package is particularly designed for bioinformaticians to assemble complex plots for publication. |
| License: | GPL-3 |
| RoxygenNote: | 7.1.2 |
| Imports: | grid, stats, colorspace, RColorBrewer |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| Language: | en-US |
| NeedsCompilation: | no |
| Packaged: | 2022-02-27 16:56:11 UTC; zhouw3 |
| Author: | Wanding Zhou [aut, cre] |
| Maintainer: | Wanding Zhou <zhouwanding@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2022-02-27 17:10:02 UTC |
merge plotting objects
Description
merge plotting objects
Usage
## S3 method for class 'WObject'
group + p
Arguments
group |
a WGroup or a plotting object |
p |
a new plotting object |
Value
a WGroup
Add a plotting object to a group
Description
The object to be added are in the same coordinate system as the group.
Usage
AddWGroup(group.obj, new.obj)
Arguments
group.obj |
WGroup object to be added to |
new.obj |
plotting object to be added |
Value
a WGroup object where new.obj is added.
Beneath
Description
Generate dimension beneath another object
Usage
Beneath(
x = NULL,
height = NULL,
pad = 0.01,
min.ratio = 0.02,
h.aln = NULL,
v.scale = NULL,
v.scale.proportional = FALSE
)
Arguments
x |
an object with dimension |
height |
the height of the new object (when NULL set proportional to the data) |
pad |
padding between the target and current |
min.ratio |
minimum ratio of dimensions when auto-scale |
h.aln |
object for horizontal alignment (when NULL, set to x) |
v.scale |
object for vertical scaling (when NULL, set to x) |
v.scale.proportional |
when v.scale is provided, whether to make proportional to data |
Value
a dimension generator beneath x
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WColorBarH(1:20, cmp=CMPar(), continuous=FALSE, Beneath())
Bottom left of
Description
Place a new object to the bottom left corner of another.
Usage
BottomLeftOf(x = NULL, just = c("right", "bottom"), v.pad = 0, h.pad = 0)
Arguments
x |
target object, either a name, a object or NULL which refers to the last plotting object |
just |
the part from the new object that should be attached to |
v.pad |
vertical translational padding [0.0] |
h.pad |
horizontal translational padding [0.0] |
Value
a WDimGenerator
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), BottomLeftOf(just=c('right','top')))
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), BottomLeftOf(just=c('right','bottom')))
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), BottomLeftOf(just=c('left','bottom')))
Bottom right of
Description
Place a new object to the bottom right corner of another.
Usage
BottomRightOf(x = NULL, just = c("left", "bottom"), v.pad = 0, h.pad = 0)
Arguments
x |
target object, either a name, a object or NULL which refers to the last plotting object |
just |
the part from the new object that should be attached to |
v.pad |
vertical translational padding [0.0] |
h.pad |
horizontal translational padding [0.0] |
Value
a WDimGenerator
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), BottomRightOf(just=c('left','top')))
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), BottomRightOf(just=c('left','bottom')))
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), BottomRightOf(just=c('right','bottom')))
Color Map Parameters
Description
Create color map parameters
Usage
CMPar(
dmin = NULL,
dmax = NULL,
brewer.name = NULL,
brewer.n = 3,
colorspace.name = NULL,
colorspace.n = 2,
cmap = NULL,
label2color = NULL,
use.data = FALSE,
stop.points = NULL,
na.color = "#C0C0C0",
rev = FALSE,
grey.scale = FALSE
)
Arguments
dmin |
minimum for continuous color map |
dmax |
maximum for continuous color map |
brewer.name |
palette name for RColorbrewer |
brewer.n |
number of stop points in RColorBrewer for continuous color map |
colorspace.name |
colorspace name |
colorspace.n |
number of stops in colorspace palettes |
cmap |
customized colormap name |
label2color |
a named vector or list that defines label to color mapping explicitly for discrete color mapping |
use.data |
use data as color, data must be either common color names or hexdecimal color names |
stop.points |
custome stop points |
na.color |
color for NA |
rev |
reverse stop points |
grey.scale |
whether to use grey scale |
Value
an object of class CMPar
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WColorBarV(1:20, cmp=CMPar(brewer.name = 'RdBu'), RightOf())
Calculate Text Bounding
Description
Calculate bounding box including texts.
Usage
CalcTextBounding(x, ...)
Arguments
x |
object |
... |
extra options |
Details
W.R.T lower left corner of the view port in the unit of points
Calculate Texting Bounding for WHeatmap
Description
Calculate Texting Bounding for WHeatmap
Usage
## S3 method for class 'WHeatmap'
CalcTextBounding(hm, group)
Arguments
hm |
an object of class WHeatmap |
group |
an object of class WGroup |
Value
an object of class WDim in coordinate points
Constructor for ColoMap object
Description
Create color maps
Usage
ColorMap(
continuous = TRUE,
colors = NULL,
dmin = NULL,
dmax = NULL,
scaler = NULL,
mapper = NULL
)
Arguments
continuous |
whether colormap is continuous |
colors |
colors for each data point |
dmin |
miminum in continuous color map |
dmax |
maximum in continuous color map |
scaler |
scaler function from data range to 0-1 |
mapper |
function that maps data to color |
Value
an object of class ColorMap
Convert from affine coordinates to absolute coordinates
Description
Convert from affine coordinates to absolute coordinates
Usage
FromAffine(dm.affine, dm.sys)
Arguments
dm.affine |
dimension on affine coordinates (relative coordinates) |
dm.sys |
dimension of the affine system |
Value
dimension on the same coordinate system
Check whether group names are unique
Description
Check whether group names are unique
Usage
GroupCheckNameUnique(group.obj)
Arguments
group.obj |
a WGroup |
Value
TRUE or FALSE
Get an plotting object from a group's descendants
Description
Get an plotting object from a group's descendants
Usage
GroupDeepGet(x, nm, force.unique = TRUE)
Arguments
x |
a WGroup object |
nm |
name |
force.unique |
assume the name is unique in the descendants and get one object instead of a list |
Value
if 'force.unique==FALSE' return a list. Otherwise, one plotting object.
LeftOf
Description
Generate dimension to the left of another object
Usage
LeftOf(
x = NULL,
width = NULL,
pad = 0.01,
min.ratio = 0.02,
v.aln = NULL,
h.scale = NULL,
h.scale.proportional = FALSE
)
Arguments
x |
an object with dimension |
width |
the width of the new object (when NULL, set proportional to data) |
pad |
padding between the target and current |
min.ratio |
minimum ratio of dimensions when auto-scale |
v.aln |
object for vertical alignment (when NULL, set to x) |
h.scale |
object for horizontal scaling (when NULL, set to x) |
h.scale.proportional |
when h.scale is provided, whether to make proportional to data |
Value
a dimension to the left of x
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WColorBarV(1:20, cmp=CMPar(), continuous=FALSE, LeftOf())
map data to continuous color
Description
map data to continuous color
Usage
MapToContinuousColors(data, cmp = CMPar(), given.cm = NULL)
Arguments
data |
numeric vector |
cmp |
an color map parameter object of class CMPar |
given.cm |
given colormap |
Value
an object of ColorMap
Examples
barplot(1:10, col=MapToContinuousColors(1:10)$colors)
barplot(1:20, col=MapToContinuousColors(c(1:10,10:1))$colors)
map data to discrete color
Description
map data to discrete color
Usage
MapToDiscreteColors(data, cmp = CMPar(), given.cm = NULL)
Arguments
data |
numeric vector |
cmp |
an color map parameter object of class CMPar |
given.cm |
given color map |
Value
an object of ColorMap
Examples
pie(rep(1,6), col=MapToDiscreteColors(c(1:3,10:13))$colors)
Resolve name to object
Description
Resolve name to object
Usage
Resolve(x, ...)
Arguments
x |
the target |
... |
extra options |
RightOf
Description
Generate dimension to the right of another object
Usage
RightOf(
x = NULL,
width = NULL,
pad = 0.01,
min.ratio = 0.02,
v.aln = NULL,
h.scale = NULL,
h.scale.proportional = FALSE
)
Arguments
x |
an object with dimension |
width |
the width of the new object (when NULL, set proportional to data) |
pad |
padding between the target and current |
min.ratio |
minimum ratio of dimensions when auto-scale |
v.aln |
object for vertical alignment (when NULL, set to x) |
h.scale |
object for horizontal scaling (when NULL, set to x) |
h.scale.proportional |
when h.scale is provided, whether to make proportional to data |
Value
a dimension to the right of x
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WColorBarV(1:20, cmp=CMPar(), continuous=FALSE, RightOf())
Scale group
Description
Scale group to incorporate text on margins
Usage
ScaleGroup(group.obj)
Arguments
group.obj |
group object that needs to be scaled |
Value
scaled group obj
Convert from absolute coordinates to affine coordinates
Description
Convert from absolute coordinates to affine coordinates
Usage
ToAffine(dm, dm.sys)
Arguments
dm |
dimension on the same coordinate system as the affine system (absolute coordinates) |
dm.sys |
dimension of the affine system |
Value
dimension on affine coordinates (relative coordinates)
Top left of
Description
Place a new object to the top left corner of another.
Usage
TopLeftOf(x = NULL, just = c("right", "bottom"), v.pad = 0, h.pad = 0)
Arguments
x |
target object, either a name, a object or NULL which refers to the last plotting object |
just |
the part from the new object that should be attached to |
v.pad |
vertical translational padding [0.0] |
h.pad |
horizontal translational padding [0.0] |
Value
a WDimGenerator
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), TopLeftOf(just=c('right','bottom')))
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), TopLeftOf(just=c('right','top')))
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), TopLeftOf(just=c('left','top')))
Top of
Description
Generate dimension top of another object
Usage
TopOf(
x = NULL,
height = NULL,
pad = 0.01,
min.ratio = 0.02,
h.aln = NULL,
v.scale = NULL,
v.scale.proportional = FALSE
)
Arguments
x |
an object with dimension |
height |
the height of the new object (when NULL, set to proportional to data) |
pad |
padding between the target and current |
min.ratio |
minimum ratio of dimensions when auto-scale |
h.aln |
object for horizontal alignment (when NULL, set to x) |
v.scale |
object for vertical scaling (when NULL, set to x) |
v.scale.proportional |
when v.scale is provided, whether to make proportional to data |
Value
a dimension generator on top of x
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WColorBarH(1:20, cmp=CMPar(), continuous=FALSE, TopOf())
Top right of
Description
Place a new object to the top right corner of another.
Usage
TopRightOf(x = NULL, just = c("left", "bottom"), v.pad = 0, h.pad = 0)
Arguments
x |
target object, either a name, a object or NULL which refers to the last plotting object |
just |
the part from the new object that should be attached to |
v.pad |
vertical translational padding [0.0] |
h.pad |
horizontal translational padding [0.0] |
Value
a WDimGenerator
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), TopRightOf(just=c('left','bottom')))
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), TopRightOf(just=c('right','top')))
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'), TopRightOf(just=c('left','top')))
WColorBarH
Description
a horizontal color bar
Usage
WColorBarH(
data,
...,
label = NULL,
label.side = "r",
label.fontsize = 12,
label.pad = 0.005,
label.space = 0.05,
label.use.data = FALSE
)
Arguments
data |
numeric vector |
... |
additional options to WHeatmap |
label |
colorbar label |
label.side |
l (for left) or r (for right) |
label.fontsize |
label font size |
label.pad |
label padding |
label.space |
when label.use.data, the space between labels |
label.use.data |
use data to show legend in situ |
Value
an object of class WColorBarH
Examples
WColorBarH(matrix(1:50))
WColorBarV
Description
a vertical color bar
Usage
WColorBarV(
data,
...,
label = NULL,
label.side = "t",
label.fontsize = 12,
label.pad = 0.005,
label.space = 0.05,
label.use.data = FALSE
)
Arguments
data |
numeric vector |
... |
additional options to WHeatmap |
label |
colorbar label |
label.side |
t (for top) or b (for bottom) |
label.fontsize |
label font size |
label.pad |
label padding |
label.space |
when label.use.data, the space between labels |
label.use.data |
use data to show legend in situ |
Value
an object of class WColorBarV
Examples
WColorBarV(matrix(50:1))
column bind non-overlapping objects
Description
column bind non-overlapping objects
Usage
WColumnBind(..., nr = NULL, nc = NULL)
Arguments
... |
plotting objects |
nr |
number of rows |
nc |
number of columns |
Value
an object of class WDim
Examples
WHeatmap(matrix(rnorm(2000),nrow=40),name='a') +
WHeatmap(matrix(rnorm(30), nrow=3), RightOf(),name='b') +
WColorBarH(1:10, TopOf(WColumnBind('a','b')))
Customize an existing plot
Description
Customize an existing plot
Usage
WCustomize(
mar.left = NULL,
mar.right = NULL,
mar.top = NULL,
mar.bottom = NULL,
mar = NULL
)
Arguments
mar.left |
left margin [0.03] |
mar.right |
right margin [0.03] |
mar.top |
top margin [0.03] |
mar.bottom |
bottom margin [0.03] |
mar |
margin in all directions [0.03] |
Value
an object of class WCustomize
Examples
WHeatmap(matrix(c('fred','frank','brad',
'frank','fred','frank'), ncol=2)) +
WLegendV(NULL, RightOf(), label.fontsize = 20) +
WCustomize(mar.right=0.1)
WDendrogram class
Description
WDendrogram class
Usage
WDendrogram(
clust = NULL,
dm = WDim(0, 0, 1, 1),
name = "",
facing = c("bottom", "top", "left", "right")
)
Arguments
clust |
hclust object |
dm |
plotting dimension |
name |
name of the dendrogram plot |
facing |
direction of the dendrogram plot |
Value
an object of class WDendrogram
Examples
WDendrogram(column.cluster(matrix(1:24,nrow=4))$column.clust)
class WDim
Description
class WDim
Usage
WDim(
left = 0,
bottom = 0,
width = 1,
height = 1,
nr = 1,
nc = 1,
text.x = 0,
text.y = 0,
text.just = c("center", "center"),
column.split = NULL,
row.split = NULL
)
Arguments
left |
left coordinate |
bottom |
bottom coordinate |
width |
width |
height |
height |
nr |
number of row |
nc |
number of column |
text.x |
x anchor for text |
text.y |
y anchor for text |
text.just |
just for text |
column.split |
a list of WDim objects for column split |
row.split |
a list of WDim objects for row split |
Value
a WDim object
WGG object form ggplot with coordinates
Description
WGG object form ggplot with coordinates
Usage
WGG(ggobj, dm = NULL, name = "")
Arguments
ggobj |
ggplot plotting object |
dm |
dimension |
name |
name |
Value
WGG object
WGrob object plot from a gList of grob objects
Description
WGrob object plot from a gList of grob objects
Usage
WGrob(glist, dm = NULL, name = "")
Arguments
glist |
gList object |
dm |
dimension |
name |
name |
Value
WGrob object
Construct a WGroup
Description
Construct a WGroup
Usage
WGroup(
...,
name = "",
group.dm = NULL,
group.from.member = FALSE,
mar = WMar(),
affine = FALSE,
nr = NULL,
nc = NULL
)
Arguments
... |
plotting objects to be grouped |
name |
name of the group |
group.dm |
group dimension, by default use the dm of the merge of members |
group.from.member |
group merged from member coordinates (require affine == FALSE), the supplied group.dm is ignored |
mar |
a WMar object |
affine |
whether the group members are on affine coordinates already |
nr |
number of rows |
nc |
number of columns |
Value
a WGroup object
WHeatmap object
Description
Create a heatmap
Usage
WHeatmap(
data = NULL,
dm = NULL,
name = "",
continuous = NULL,
cmp = NULL,
cm = NULL,
xticklabels = NULL,
xticklabels.n = NULL,
xticklabel.side = "b",
xticklabel.fontsize = 12,
xticklabel.rotat = 90,
xticklabel.pad = 0.005,
xticklabel.space = 0.05,
xticklabel.use.data = FALSE,
yticklabels = NULL,
yticklabels.n = NULL,
yticklabel.side = "l",
yticklabel.fontsize = 12,
yticklabel.rotat = 0,
yticklabel.pad = 0.005,
yticklabel.space = 0.05,
yticklabel.use.data = FALSE,
sub.name = NULL,
bbox = FALSE,
gp = NULL
)
Arguments
data |
data matrix |
dm |
plotting dimension (a WDim or a WDimGenerator object) |
name |
name of the plot |
continuous |
whether the data should be treated as continuous or discrete |
cmp |
a CMPar object, for tunning color mapping parameters |
cm |
a given color map |
xticklabels |
to plot xtick labels, one may supply characters to plot just a subset of xtick labels |
xticklabels.n |
number of xtick labels to plot (resample for aethetics by default) |
xticklabel.side |
xticklabel side (t or b) |
xticklabel.fontsize |
xticklabel font size |
xticklabel.rotat |
xticklabel rotation |
xticklabel.pad |
padding between xticklabel and x-axis |
xticklabel.space |
xticklabel space |
xticklabel.use.data |
use data to label x-axis (most likely used by colorbar) |
yticklabels |
to plot ytick labels, one may supply characters to plot just a subset of ytick labels |
yticklabels.n |
number of ytick labels to plot (resample for aethetics by default) |
yticklabel.side |
yticklabel side (l or r) |
yticklabel.fontsize |
yticklabel font size |
yticklabel.rotat |
yticklabel rotation |
yticklabel.pad |
padding between yticklabel and y-axis |
yticklabel.space |
yticklabel space |
yticklabel.use.data |
use data to label y-axis (most likely used by colorbar) |
sub.name |
subclass name |
bbox |
whether to plot the boundary box (useful with white matrix elements) |
gp |
a list of graphical parameters |
Value
one or a list of heatmaps (depends on whether dimension is split)
Examples
WHeatmap(matrix(1:10, nrow=2), cmp=CMPar(brewer.name='Greens'))
WHeatmap(matrix(1:12,nrow=2), cmp=CMPar(brewer.name='Greens'), name='a') +
WHeatmap(matrix(1:6,nrow=1), Beneath(pad=0.05), cmp=CMPar(brewer.name='Set2'), name='b') +
WHeatmap(matrix(c(1:30,30:1),nrow=5), Beneath(pad=0.05), 'c', cmp=CMPar(cmap='jet')) +
WHeatmap(matrix(1:24,nrow=4), RightOf('c'), 'd', cmp=CMPar(brewer.name='Set1')) +
WLegendV('c', LeftOf('c', pad=0.01), yticklabel.side='l') +
WLegendV('b', RightOf('b', width=0.1)) +
WLegendV('a', RightOf('a')) +
WHeatmap(matrix(1:100, nrow=10), RightOf('d'), cmp=CMPar(brewer.name='RdYlGn')) +
WColorBarH(matrix(5:1), TopOf(), cmp=CMPar(colorspace.name = 'diverge_hcl')) +
WColorBarH(matrix(50:1), TopOf(), cmp=CMPar(colorspace.name = 'terrain_hcl')) +
WColorBarH(matrix(1:8), TopOf(), cmp=CMPar(colorspace.name = 'sequential_hcl')) +
WColorBarH(matrix(1:8), TopOf(), cmp=CMPar(brewer.name = 'YlOrRd'))
## One could use %>% too, in combination with magrittr's add function
## Not run:
library(magrittr)
WColorBarH(1:10) %>% add(WColorBarV(rep(c('black','red','blue'),3), RightOf()))
## End(Not run)
construct a WLabel
Description
construct a WLabel
Usage
WLabel(
x = NULL,
dm = WDim(),
name = "",
fontsize = 12,
rot = 0,
color = "black"
)
Arguments
x |
text to be labeled |
dm |
position |
name |
name |
fontsize |
font size |
rot |
rotation |
color |
color of the label |
Value
a WLabel object
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) + WLabel("This is a label.", RightOf(), rot=-90)
WLegendH
Description
a horizontal legend
Usage
WLegendH(
x = NULL,
dm = NULL,
name = "",
n.stops = 20,
n.text = 5,
label.fontsize = 12,
width = 0.02,
height = 0.05,
decreasing = TRUE,
...
)
Arguments
x |
a name or a plotting object, if NULL use the last plotting object |
dm |
position |
name |
name of the plotted legend |
n.stops |
number of stops in computing continuous legend |
n.text |
number of text labels in continuous legend |
label.fontsize |
label font size |
width |
width of each unit in plotted legend |
height |
height of each unit in plotted legend |
decreasing |
reversed color map |
... |
additional options to WHeatmap |
Value
an object of class WLegendH
Examples
WHeatmap(matrix(1:4,nrow=2))+WLegendH(NULL, Beneath())
WLegendV
Description
a vertical legend
Usage
WLegendV(
x = NULL,
dm = NULL,
name = "",
n.stops = 20,
n.text = 5,
label.fontsize = 12,
width = 0.05,
height = 0.02,
decreasing = FALSE,
...
)
Arguments
x |
a name or a plotting object, if NULL use the last plotting object |
dm |
position |
name |
name of the plotted legend |
n.stops |
number of stops in computing continuous legend |
n.text |
number of text labels in continuous legend |
label.fontsize |
label font size |
width |
width of each unit in plotted legend |
height |
height of each unit in plotted legend |
decreasing |
reversed color map |
... |
additional options to WHeatmap |
Value
an object of class WLegendV
Examples
WHeatmap(matrix(1:4,nrow=2))+WLegendV(NULL, RightOf())
plot multiple figures in a matrix
Description
This function can take WObject, or gg (from ggplot) since the coordinates are not set, gg can be converted to WGG
Usage
WMatrix(objs, ncols = 1)
Arguments
objs |
a list of plotting objects either WObject or gg |
ncols |
number of columns |
Value
WGroup
Construct a WObject
Description
Construct a WObject
Usage
WObject(dm = NULL, name = "")
Arguments
dm |
position |
name |
name |
Value
a WObject
place an arbitrary position w.r.t a subplot
Description
place an arbitrary position w.r.t a subplot
Usage
WPosition(
anchor.x,
anchor.y,
x = NULL,
just = c("left", "bottom"),
data.coord = FALSE
)
Arguments
anchor.x |
x coordinates |
anchor.y |
y coordinates |
x |
plotting object to anchor |
just |
adjustment of new plot |
data.coord |
whether the coordinates is in term of data |
Value
a WDimGenerator object
Examples
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(c(rnorm(100)+1,rnorm(100)), nrow=10),
cmp=CMPar(brewer.name = 'RdGy'),
WPosition(0.1,0.1,just=c('left','top')))
construct a WRect
Description
construct a WRect
Usage
WRect(
obj = NULL,
x.span = NULL,
y.span = NULL,
color = "black",
lwd = 3,
fill = NA,
name = ""
)
Arguments
obj |
a plotting object or its name |
x.span |
x-axis/horizontal span (e.g., c(2,4)) |
y.span |
y-axis/vertical span (e.g., c(5,9)) |
color |
edge color |
lwd |
edge width |
fill |
fill color |
name |
name |
Value
a WRect object
row bind non-overlapping objects
Description
row bind non-overlapping objects
Usage
WRowBind(..., nr = NULL, nc = NULL)
Arguments
... |
plotting objects |
nr |
number of rows |
nc |
number of columns |
Value
an object of class WDim
Examples
WHeatmap(matrix(rnorm(2000),nrow=40),name='a') +
WHeatmap(matrix(rnorm(30), nrow=3), Beneath(),name='b') +
WColorBarV(1:10, LeftOf(WRowBind('a','b')))
subset WGroup
Description
subset WGroup
Usage
## S3 method for class 'WGroup'
x[i]
Arguments
x |
a WGroup object |
i |
integer indexing element |
Value
a subset of WGroup or NULL
row- and column-cluster a matrix
Description
row- and column-cluster a matrix
Usage
both.cluster(
mat,
extra.row = NULL,
extra.column = NULL,
hc.method = "ward.D2",
dist.method = "euclidean"
)
Arguments
mat |
input matrix |
extra.row |
extra row reordering |
extra.column |
extra column reordering |
hc.method |
method to use in hclust |
dist.method |
method to use in dist |
Value
a list of clustered row, column and matrix
Examples
WHeatmap(both.cluster(matrix(rnorm(100),nrow=10))$mat)
column cluster a matrix
Description
column cluster a matrix
Usage
column.cluster(mat, ..., hc.method = "ward.D2", dist.method = "euclidean")
Arguments
mat |
input matrix |
... |
extra color bars or matrix that needs column reordered |
hc.method |
method to use in hclust |
dist.method |
method to use in dist |
Value
a list of clustered row, column and matrix
Examples
WHeatmap(column.cluster(matrix(rnorm(100),nrow=10))$mat)
darker jet color stops
Description
darker jet color stops
Usage
darkjet.stops
Format
An object of class character of length 6.
Get dimensions
Description
Get dimensions
Usage
getdim(x)
Arguments
x |
WDim object or a plotting object |
Value
vector of dimensions
Draw dendrogram under grid system
Description
The dendrogram can be renderred. A viewport is created which contains the dendrogram.
Usage
grid.dendrogram(
dend,
facing = c("bottom", "top", "left", "right"),
max_height = NULL,
order = c("normal", "reverse"),
...
)
Arguments
dend |
a stats::dendrogram object. |
facing |
facing of the dendrogram. |
max_height |
maximum height of the dendrogram. |
order |
order |
... |
additional options |
Details
-order should leaves of dendrogram be put in the normal order (1, ..., n) or reverse order (n, ..., 1)? -... pass to 'grid::viewport' which contains the dendrogram.
This function only plots the dendrogram without adding labels. The leaves of the dendrogram locates at unit(c(0.5, 1.5, ...(n-0.5))/n, "npc").
Value
view port that plots dendrogram
jet color stops
Description
jet color stops
Usage
jet.stops
Format
An object of class character of length 75.
show layout
Description
show layout
Usage
ly(x)
Arguments
x |
plot |
Examples
ly(
WHeatmap(matrix(rnorm(2000),nrow=40)) +
WHeatmap(matrix(rnorm(2000),nrow=40), cmp=CMPar(brewer.name = 'RdBu'),
BottomRightOf(just=c('left','top'))))
print a dendrogram
Description
print a dendrogram
Usage
## S3 method for class 'WDendrogram'
print(x, stand.alone = TRUE, layout.only = FALSE, cex = 1, ...)
Arguments
x |
a dendrogram |
stand.alone |
plot is stand alone |
layout.only |
plot layout only |
cex |
factor to scaling texts |
... |
additional options (ignored) |
Value
view port that contains the plotted dendrogram
Examples
WDendrogram(column.cluster(matrix(1:24,nrow=4))$column.clust)
plot WGG object
Description
plot WGG object
Usage
## S3 method for class 'WGG'
print(x, cex = 1, layout.only = FALSE, stand.alone = TRUE, ...)
Arguments
x |
WGG |
cex |
scaling factor for text |
layout.only |
plot layout |
stand.alone |
produce a stand.alone plot |
... |
extra options |
Value
printed ggobj object
print a WGenerator
Description
This calls WGenerator and creates a WGroup to enclose the produced object.
Usage
## S3 method for class 'WGenerator'
print(x, ...)
Arguments
x |
a WGenerator object |
... |
additional options |
Value
the WGroup containing the plotting object
plot WGrob object
Description
plot WGrob object
Usage
## S3 method for class 'WGrob'
print(x, cex = 1, layout.only = FALSE, stand.alone = TRUE, ...)
Arguments
x |
WGrob |
cex |
scaling factor for text |
layout.only |
plot layout |
stand.alone |
produce a stand.alone plot |
... |
extra options |
Draw WGroup
Description
Draw WGroup
Usage
## S3 method for class 'WGroup'
print(x, stand.alone = TRUE, cex = 1, layout.only = FALSE, ...)
Arguments
x |
a WGroup |
stand.alone |
to plot stand alone |
cex |
factor for scaling fonts |
layout.only |
to plot layout only |
... |
additional options |
plot WHeatmap
Description
plot WHeatmap
Usage
## S3 method for class 'WHeatmap'
print(x, cex = 1, layout.only = FALSE, stand.alone = TRUE, ...)
Arguments
x |
a WHeatmap |
cex |
factor to scaling texts |
layout.only |
plot layout only |
stand.alone |
plot is stand alone |
... |
additional options |
Value
NULL
Examples
print(WHeatmap(matrix(1:12, nrow=2)))
print WLabel
Description
print WLabel
Usage
## S3 method for class 'WLabel'
print(x, cex = 1, layout.only = FALSE, stand.alone = TRUE, ...)
Arguments
x |
a WLabel object |
cex |
factor to scale text |
layout.only |
plot layout only |
stand.alone |
plot label stand alone |
... |
additional options |
Examples
print(WLabel("This is a label."))
print WRect
Description
print WRect
Usage
## S3 method for class 'WRect'
print(x, cex = 1, layout.only = FALSE, stand.alone = TRUE, ...)
Arguments
x |
a WRect object |
cex |
factor for scaling text |
layout.only |
print layout only |
stand.alone |
plot WRect standalone |
... |
additional options |
Value
the WRect object
row cluster a matrix
Description
row cluster a matrix
Usage
row.cluster(mat, ..., hc.method = "ward.D2", dist.method = "euclidean")
Arguments
mat |
input matrix |
... |
extra color bars or matrix that needs row reordered. |
hc.method |
method to use in hclust |
dist.method |
method to use in dist |
Value
a list of clustered row, column and matrix
Examples
WHeatmap(row.cluster(matrix(rnorm(100),nrow=10))$mat)