plotProportionBar
creates bar plots comparing the
cross-category proportion. plotProportionDot
creates dot plots.
plotClusterProportions
has variable pre-specified and calls the dot
plot. plotProportion
produces a combination of both bar plots and dot
plot.
Having package "ggrepel" installed can help adding tidier percentage annotation on the pie chart.
Usage
plotProportion(
object,
class1 = NULL,
class2 = "dataset",
method = c("stack", "group", "pie"),
...
)
plotProportionDot(
object,
class1 = NULL,
class2 = "dataset",
showLegend = FALSE,
panelBorder = TRUE,
...
)
plotProportionBar(
object,
class1 = NULL,
class2 = "dataset",
method = c("stack", "group"),
inclRev = FALSE,
panelBorder = TRUE,
combinePlot = TRUE,
...
)
plotClusterProportions(object, useCluster = NULL, return.plot = FALSE, ...)
plotProportionPie(
object,
class1 = NULL,
class2 = "dataset",
labelSize = 4,
labelColor = "white",
...
)
Arguments
- object
A liger object.
- class1, class2
Each should be a single name of a categorical variable available in
cellMeta
slot. Number of cells in each categories inclass2
will be served as the denominator when calculating proportions. By defaultclass1 = NULL
and uses default clusters andclass2 = "dataset"
.- method
For bar plot, choose whether to draw
"stack"
or"group"
bar plot. Default"stack"
.- showLegend, panelBorder, ...
ggplot theme setting arguments passed to
.ggplotLigerTheme
.- inclRev
Logical, for barplot, whether to reverse the specification for
class1
andclass2
and produce two plots. DefaultFALSE
.- combinePlot
Logical, whether to combine the two plots with
plot_grid
when two plots are created. DefaultTRUE
.- useCluster
For
plotClusterProportions
. Same asclass1
whileclass2
is hardcoded with"dataset"
.- return.plot
defuncted.
- labelSize, labelColor
Settings on pie chart percentage label. Default
4
and"white"
.