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Visualize Subtype Prediction Scores in a Sorted/ranked/stacked Barplot

plot_subscore_box.Rd

Visualize subtype prediction score within a set subtype in a stacked barplot.

Usage

plot_subscore_box(
  these_predictions,
  this_subtype,
  out_path = NULL,
  out_format = "png",
  plot_width = 4,
  plot_height = 4,
  return_data = FALSE
)

Arguments

these_predictions

Required parameter, should be the output from classify_samples().

this_subtype

Required parameter. Should be one of the set subtype classes from the LundTax nomenclature.

out_path

Optional, set path to export plot.

out_format

Required parameter if out_path is specified. Can be "png" (default) or "pdf". The user can further specify the dimensions of the returned plot with plot_width and plot_height.

plot_width

This parameter controls the width in inches. Default is 4 (1200 pixels at 300 PPI).

plot_height

This parameter controls the height in inches. Default is 4 (1200 pixels at 300 PPI).

return_data

Set to TRUE to return tidy data used by the plotting function. Default is FALSE.

Value

Nothing.

Details

Take the output from classify_samples and return a stacked barplot plot representing the distribution of the, for that class, subtype prediction score. Set the subtype of desire with this_subtype. The subtype can be one of the subtypes included in the LundTax subtype classification nomenclature.

Examples

#run predictor
sjodahl_classes = classify_samples(this_data = sjodahl_2017, 
                                   log_transform = FALSE, 
                                   adjust = TRUE, 
                                   impute = TRUE, 
                                   include_data = TRUE, 
                                   verbose = FALSE)
#plot Uro scores
plot_subscore_box(these_predictions = sjodahl_classes, 
                  this_subtype = "Uro")


#plot UroA scores
plot_subscore_box(these_predictions = sjodahl_classes, 
                  this_subtype = "UroA")


#return data
plot_data = plot_subscore_box(these_predictions = sjodahl_classes, 
                              this_subtype = "Uro", 
                              return_data = TRUE)
#> No plot generated, returning tidy data instead...

#view data
head(plot_data)
#> # A tibble: 6 × 3
#>   sample_id subtype value
#>   <fct>     <fct>   <dbl>
#> 1 15.CEL    Uro         1
#> 2 15.CEL    GU          0
#> 3 15.CEL    BaSq        0
#> 4 15.CEL    Mes         0
#> 5 15.CEL    ScNE        0
#> 6 45.CEL    Uro         1