swimmer_plot: Creating the base of a swimmers plot

In swimplot: Tools for Creating Swimmers Plots using 'ggplot2'

Description

This function allows you to create swimmers plots with bars, includes options to have the bars change colours and create stratified plots

Usage

swimmer_plot(
  df,
  id = "id",
  end = "end",
  start = "start",
  name_fill = NULL,
  name_col = NULL,
  name_alpha = NULL,
  increasing = TRUE,
  id_order = NULL,
  stratify = FALSE,
  base_size = 11,
  identifiers = TRUE,
  ...
)

Arguments

df	a data frame
id	column name for id, default is 'id'
end	column name with the bar lengths (or bar end positions if bars change colour), default is 'end'
start	column name with the bar start positions (only required when there are gaps between sections of bars, or bars which do not start at zero), default is 'start'
name_fill	a column name to map the bar fill
name_col	a column name to map the bar colour
name_alpha	a column name to map the bar transparency
increasing	Binary to specify bars in increasing order (Default is TRUE)
id_order	order of the bars by id, can input a column name to sort by, or the ids in order.
stratify	a list of column names to stratify by
base_size	the base size for the plot, default is 11
identifiers	Binary to specify patient identifiers are included in the y axis (default is TRUE)
...	additional geom_col() arguments

Value

a swimmer plot with bars

See Also

swimmer_points swimmer_lines swimmer_lines swimmer_points_from_lines swimmer_arrows swimmer_text

Examples

swim_plot <-
swimmer_plot(df=ClinicalTrial.Arm,id='id',end='End_trt',name_fill='Arm',col="black",id_order='Arm')

# Add ggplot layers to improve the plot's aesthetic

swim_plot +
ggplot2::scale_fill_manual(name="Treatment",values=c("#e41a1c", "#377eb8","#4daf4a"))+
ggplot2::ylab('Time (Days)')



#Example with Stratification

swim_plot_stratify <- swimmer_plot(df=ClinicalTrial.Arm,id='id',end='End_trt',name_fill='Arm',
col="black",alpha=0.75,width=.8,base_size = 18,stratify= c('Age','Sex'))

swim_plot_stratify +
ggplot2::scale_fill_manual(name="Treatment",values=c("#e41a1c", "#377eb8","#4daf4a"))+
ggplot2::ylab('Time (Days)')

#Example when there are gaps between the bars and bars do not start at zero

#Both a start and end time need to be specified when there are gaps between sections of bars

Gap_data <- data.frame(patient_ID=c('ID:3','ID:1','ID:1','ID:1','ID:2',
                                   'ID:2','ID:2','ID:3','ID:3','ID:2'),
                      start=c(10,1,2,7,2,10,14,5,0,22),
                      end=c(20,2,4,10,7,14,22,7,3,26),
                      treatment=c("A","B","C","A","A","C","A","B","C",NA))

swimmer_plot(df=Gap_data,id='patient_ID',name_fill="treatment",col=1,identifiers=FALSE,
id_order = c('ID:1','ID:2','ID:3')) +
ggplot2::theme_bw()+ggplot2::scale_fill_manual(name="Treatment",
values=c("A"="#e41a1c", "B"="#377eb8","C"="#4daf4a",na.value=NA),breaks=c("A","B","C"))+
 ggplot2::scale_y_continuous(breaks=c(0:26))

swimplot documentation built on March 31, 2021, 1:06 a.m.