Subtype Forest Plot — plot_subtype

Create a subtype aware forest plot, with a set clinical end-point.

Usage

plot_subtype_forest(
  these_predictions = NULL,
  these_samples_metadata = NULL,
  this_subtype = NULL,
  subtype_class = "5_class",
  surv_event = NULL,
  sig_color = "red",
  significant_p = 0.05,
  surv_time = NULL,
  sample_id_col = NULL,
  row_to_col = FALSE,
  plot_title = NULL,
  plot_subtitle = NULL,
  plot_caption = NULL,
  plot_width = 7,
  plot_height = 7,
  out_format = "png",
  out_path = NULL,
  file_name = NULL,
  return_data = FALSE
)

Arguments

these_predictions: Required parameter if this_metadata is not provided. Should be output from classify_samples().
these_samples_metadata: Required parameter if these_predictions is not provided or to provide survival data. Metadata associated with the prediction output.
this_subtype: A character vector specifying the subtypes to be included in the plot. Default is c("UroA", "UroB", "UroC", "Uro", "GU", "BaSq", "Mes", "ScNE").
subtype_class: Can be one of the following; 5_class or 7_class. Default is 5_class.
surv_event: A string specifying the column name for the survival event.
sig_color: Color for annotating significant signatures. Default is red.
significant_p: Numeric parameter for flagging significant p values. Default is 0.05.
surv_time: A string specifying the column name for the survival time.
sample_id_col: Optional parameter. Allows the user to manually specify the name of a column with sample ID.
row_to_col: Optional parameter, set to TRUE to convert row names in metadata to a new column called sample_id. Default is FALSE.
plot_title: A string specifying the title of the plot.
plot_subtitle: A string specifying the subtitle of the plot.
plot_caption: A string specifying the caption of the plot.
plot_width: A numeric value specifying the width of the plot. Default is 7.
plot_height: A numeric value specifying the height of the plot. Default is 7.
out_format: A string specifying the output format of the plot ("png" or "pdf"). Default is "png".
out_path: A string specifying the output path for saving the plot.
file_name: A string specifying the file name for the saved plot.
return_data: Set to TRUE to return plot data, default is FALSE.

Value

A combined plot object if out_path is NULL. Otherwise, the plot is saved to the specified path.

Details

This function creates a forest plot for multiple subtypes based on Cox proportional hazards models. It also includes a table with the number of samples and progression events for each subtype.

Examples

#run classifier
sjodahl_classes = classify_samples(this_data = sjodahl_2017, 
                                   log_transform = FALSE, 
                                   adjust = TRUE, 
                                   impute = TRUE, 
                                   include_data = TRUE, 
                                   verbose = FALSE)
#UroA
plot_subtype_forest(these_samples_metadata = sjodahl_2017_meta,
                    these_predictions = sjodahl_classes,
                    this_subtype = "UroA",
                    subtype_class = "7_class",
                    surv_event = "surv_css_event",
                    surv_time = "surv_css_time")
#> `height` was translated to `width`.


#all 5 class subtypes
plot_subtype_forest(these_samples_metadata = sjodahl_2017_meta,
                    these_predictions = sjodahl_classes,
                    this_subtype = NULL,
                    subtype_class = "5_class",
                    surv_event = "surv_css_event",
                    surv_time = "surv_css_time")
#> `height` was translated to `width`.


#return data
forest_data = plot_subtype_forest(these_samples_metadata = sjodahl_2017_meta,
                                  these_predictions = sjodahl_classes,
                                  subtype_class = "5_class",
                                  this_subtype = c("Uro", "GU", "BaSq", "Mes", "ScNE"),
                                  return_data = TRUE,
                                  surv_event = "surv_css_event",
                                  surv_time = "surv_css_time")
#> No plot generated, returning data instead...
                                  
#view data
head(forest_data)
#>   subtype   p_value     ratio  conf_2.5 conf_97.5     significant
#> 1     Uro 0.5400061 0.8870096 0.6044836  1.301584 not significant
#> 2      GU 0.5825919 1.1360788 0.7207983  1.790619 not significant
#> 3    BaSq 0.5707407 1.1456109 0.7160574  1.832848 not significant
#> 4     Mes 0.4644418 1.3314314 0.6183662  2.866763 not significant
#> 5    ScNE 0.2916031 0.6418849 0.2815931  1.463162 not significant