aba_plot_metric: Plot metrics of an aba model summary

In ncullen93/abaR: Automated Biomarker Analysis

Plot metrics of an aba model summary

Description

Plot metrics of an aba model summary

Usage

aba_plot_metric(
  model_summary,
  metric = NULL,
  axis = c("predictor", "outcome", "group"),
  coord_flip = FALSE,
  include_basic = TRUE,
  sort = FALSE,
  facet_labels = TRUE,
  palette = "jama",
  plotly = FALSE
)

Arguments

model_summary	an aba model summary. The object to plot - this should be the result of an aba_summary() call.
metric	string. The metric to plot.
axis	string. Specifies the x axis variable, color/fill variable, and facet variable in that order. Should be a vector of length three that includes only "predictor", "outcome", and "group" as values.
coord_flip	logical. Whether to flip the x and y axes. This can be useful when there are a large amount of predictor sets and you want to view metrics vertically.
include_basic	logical. Whether to include basic predictor.
sort	logical. Whether to sort axis labels by metric value
facet_labels	logical. Whether to include facet labels or not.
palette	string. Which ggpubr palette to use. See ggpubr::set_palette.
plotly	logical. Whether to use plot.ly instead of standard ggplot. Defaults to false. Using ggplotly can be useful if you want interactivity on web pages.

Value

a ggplot of the specified aba model summary metric.

Examples

# fit aba model
model <- aba_model() %>%
  set_data(adnimerge %>% dplyr::filter(VISCODE == 'bl')) %>%
  set_groups(everyone()) %>%
  set_outcomes(ConvertedToAlzheimers, CSF_ABETA_STATUS_bl,
               .labels=c('Conversion to AD', 'CSF Abeta Status')) %>%
  set_predictors(
    PLASMA_ABETA_bl, PLASMA_PTAU181_bl, PLASMA_NFL_bl,
    c(PLASMA_ABETA_bl, PLASMA_PTAU181_bl, PLASMA_NFL_bl),
    .labels = c('A','T','N','ATN')
  ) %>%
  set_stats(stat_glm(std.beta=TRUE)) %>%
  fit()

# summarise aba model to calculate metrics
model_summary <- model %>% aba_summary()

# plot the metrics using default (defaults to AUC)
metric_plot <- model_summary %>% aba_plot_metric()

# coord flip
metric_plot2 <- model_summary %>% aba_plot_metric(coord_flip=TRUE)

# compare predictor sets within each outcome instead of the opposite
metric_plot3 <- model_summary %>%
  aba_plot_metric(axis = c('outcome','predictor', 'group'))

ncullen93/abaR documentation built on Feb. 8, 2024, 12:01 p.m.