aba_plot_metric: Plot metrics of an aba model summary

In aba: Automated Biomarker Analysis

Description

Plot metrics of an aba model summary

Usage

aba_plot_metric(
  object,
  metric = NULL,
  x = "predictor",
  group = "outcome",
  facet = "group",
  coord_flip = FALSE,
  palette = "jama",
  plotly = FALSE
)

Arguments

object	an aba model summary. The object to plot - this should be the result of an aba_summary() call.
metric	string. The performance metric to plot (e.g., AIC, AUC, adj.r.squared)
x	string. The model spec factor to use as the x axis. Defaults to predictor sets.
group	string. The model spec factor to use as the group variable in ggplot - this corresponding to "group", "fill", and "color" in ggplot. Defaults to outcome.
facet	string. The model spec factor to use as the group variable in ggplot - this corresponding to "facet_wrap" in ggplot. Defaults to group.
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.
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) %>%
  set_predictors(
    PLASMA_ABETA_bl, PLASMA_PTAU181_bl, PLASMA_NFL_bl,
    c(PLASMA_ABETA_bl, PLASMA_PTAU181_bl, PLASMA_NFL_bl)
  ) %>%
  set_stats('glm') %>%
  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(x = 'outcome', group='predictor')

aba documentation built on Dec. 17, 2021, 1:06 a.m.