knitr::opts_chunk$set(echo = TRUE, collapse = TRUE) library(dplyr) library(ggplot2) library(maraca)
The maraca package also contains an additional plot
called "component_plot"
. This one allows to plot the
different components that make up the win odds calculation.
More specifically, for each outcome, the plot shows how
often patients in each treatment arm "won" against the other
arm. For the time-to-event endpoints, this means counting how many
patients of the other arm had no more prioritized event prior.
For the continuous outcome this means counting how many patients had a lower value.
The results are separated for each outcome (non-cumulative)
and also include ties (patients from 2 treatment arms having same
outcome at the same time/same continuous outcome value).
Let us first read in some data.
library(maraca) data(hce_scenario_a)
In order to use the component_plot
, we have to first create a
maraca
object. Important here is to set the argument
compute_win_odds = TRUE
, so that the necessary calculations
are included.
maraca_dat <- maraca( data = hce_scenario_a, step_outcomes = c("Outcome I", "Outcome II", "Outcome III", "Outcome IV"), last_outcome = "Continuous outcome", fixed_followup_days = 3 * 365, column_names = c(outcome = "GROUP", arm = "TRTP", value = "AVAL0"), arm_levels = c(active = "Active", control = "Control"), # Make sure to calculate the win odds compute_win_odds = TRUE )
Now we can just plot the object using the component_plot()
function.
component_plot(maraca_dat)
It is also possible to use the component_plot()
function directly on
an hce
object (created using the
hce package).
library(hce) Rates_A <- c(1.72, 1.74, 0.58, 1.5, 1) Rates_P <- c(2.47, 2.24, 2.9, 4, 6) hce_dat <- simHCE(n = 2500, TTE_A = Rates_A, TTE_P = Rates_P, CM_A = -3, CM_P = -6, CSD_A = 16, CSD_P = 15, fixedfy = 3, seed = 31337) component_plot(hce_dat)
Furthermore, there is a plot called "cumulative_plot"
.
Similar to the component_plot
, this plot shows the different HCE components that
make up the win odds calculation. Different to the component plot,
this plot provides insight into the contributed effect for each of the components as
they are added in sequence (from top to bottom).
Additionally, there is also a right-hand panel that shows a forest plot with the win odds
and win ratio corresponding to the same cumulative sequence. To understand the contribution
from each outcome, we artificially set all the less prioritized outcomes as ties and calculate
the win odds/ratio. Thus, for each added outcome there will be less ties.
As before, in order to use the cumulative_plot
, we have to first create a
maraca
object. Important here is to set the argument
compute_win_odds = TRUE
, so that the necessary calculations
are included.
maraca_dat <- maraca( data = hce_scenario_a, step_outcomes = c("Outcome I", "Outcome II", "Outcome III", "Outcome IV"), last_outcome = "Continuous outcome", fixed_followup_days = 3 * 365, column_names = c(outcome = "GROUP", arm = "TRTP", value = "AVAL0"), arm_levels = c(active = "Active", control = "Control"), # Make sure to calculate the win odds compute_win_odds = TRUE )
Now we can just plot the object using the cumulative_plot()
function.
cumulative_plot(maraca_dat)
It is also possible to use the cumulative_plot()
function directly on
an hce
object (created using the
hce package).
cumulative_plot(hce_dat)
The user can also choose to only display one of the statistics (win odds or win ratio)
by specifying so in the include
parameter.
cumulative_plot(maraca_dat, include = "win odds")
The y-axis can easily be reversed using the reverse
parameter.
cumulative_plot(hce_dat, reverse = TRUE)
The resulting plot for the component_plot()
functions
is a normal ggplot2 object that can be styled accordingly.
component_plot(maraca_dat) + ggplot2::scale_fill_manual(values = c("seagreen", "red", "grey"), name = NULL)
Note that the cumulative_plot()
function is using the
patchwork package to combine 2 ggplot2 objects - the
bar plot and the forest plot that together make up the
cumulative_plot()
. They
can be accessed as list items and styled accordingly.
p <- cumulative_plot(maraca_dat) # Accessing the first ggplot2 object and adding styling (bar plot) p[[1]] <- p[[1]] + ggplot2::scale_fill_manual(values = c("seagreen", "red", "grey"), name = NULL) p
For the users convenience, there are also different themes available to style the plot.
The default style is called theme = "maraca"
.
component_plot(maraca_dat, theme = "maraca")
There are 2 different themes with different color
schemes, theme = "color1"
and theme = "color2"
.
cumulative_plot(maraca_dat, theme = "color1")
component_plot(maraca_dat, theme = "color2")
There is also a theme without any styling theme = "none"
that
can be used as a base when the user wants to style the plot themselves.
cumulative_plot(maraca_dat, theme = "none")
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