geom_fan: Fan plots for trend and population visualizations

In cytofan: Plot Fan Plots for Cytometry Data using 'ggplot2'

Description

Visualise the distribution of continuous variables by dividing each variables into a fixed number of bins and returning the bin limits. In fan plots ('geom_fan') bins are grouped over all variables and colored after their distance from the center bin, which corresponds to the median. The center bin corresponds to the strongest shade of 'colorbase', while other bins get decreasing shades.

Usage

geom_fan(mapping = NULL, data = NULL, position = "identity",
  na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, step = 0.01,
  colorbase = "Oranges", ...)

stat_fan(mapping = NULL, data = NULL, geom = NULL,
  position = "identity", na.rm = FALSE, show.legend = NA,
  inherit.aes = TRUE, step = 0.01, ...)

Arguments

mapping	Set of aesthetic mappings created by aes() or aes_(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
data	The data to be displayed in this layer. There are three options: If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot(). A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created. A function will be called with a single argument, the plot data. The return value must be a data.frame., and will be used as the layer data.
position	Position adjustment, either as a string, or the result of a call to a position adjustment function.
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
show.legend	logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().
step	the number of quantiles to use to compute bins
colorbase	the colors to use to draw the ribbon. defaults to RColorBrewer 'Oranges'. See brewer.pal for details.
...	Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like color = "red" or size = 3. They may also be parameters to the paired geom/stat.
geom	The geometric object to use display the data

Details

'stat_fan' is suitable only for continuous y data. Moreover, if you have less than '1/step' points you might need to adjust the 'step' parameter.

Computed variables

ymin

the lower limit of the quantile

ymax

the upper limit of the quantile

id

an identifier for the quantile

percent

the fill colorto use in geom_fan

Examples

# reformat dataset from short-wide to tall-skinny
EuStockMarkets_ts <- lapply(colnames(EuStockMarkets),function(id) {
  data.frame(id=id,value=as.numeric(EuStockMarkets[,id]))
})
EuStockMarkets_ts <- do.call('rbind',EuStockMarkets_ts)

# plot the distribution of the different stock markets
ggplot(EuStockMarkets_ts,aes(x=id,y=value))+
  geom_fan()

# Change the step
ggplot(EuStockMarkets_ts,aes(x=id,y=value))+
  geom_fan(step=0.05)

# change the default color
ggplot(EuStockMarkets_ts,aes(x=id,y=value))+
  geom_fan(colorbase='Greens')

# any valid RColorBrewer palette will work
ggplot(EuStockMarkets_ts,aes(x=id,y=value))+
  geom_fan(colorbase='RdYlGn')

cytofan documentation built on May 2, 2019, 3:58 a.m.