Plot Ranked Signature Scores in Subtypes — plot_ranked

Return a point plot with ranked scores for a set variable.

Usage

plot_ranked_score(
  these_predictions = NULL,
  this_data = NULL,
  this_score = NULL,
  this_subtype = NULL,
  subtype_class = NULL,
  seg_plot = FALSE,
  seg_width = 0.1,
  add_stat = FALSE,
  out_path = NULL,
  out_format = "png",
  plot_width = 8,
  plot_height = 5,
  plot_title = NULL,
  return_data = FALSE
)

Arguments

these_predictions: Required parameter, if no data provided with this_data. Predictions returned with classify_samples().
this_data: Optional parameter, makes it possible for the user to give the plotting function their own data, preferably retrieved with this function with return_data = TRUE. If provided, the plotting function will disregard any other parameters and only draw the plot using the data provided.
this_score: Required parameter, should be one of the numeric columns in the scores data frame from the list returned with classify_samples().
this_subtype: Optional parameter, lets the user subset the return to a specific subtype. If nopt provided, all subtypes within the selected class will be returned.
subtype_class: Required, one of the following; 5_class or 7_class. Needed for coloring the points based on subtype classification.
seg_plot: Boolean parameter, set to TRUE to return a segment plot with ranked scores for the selected subtype class. Default is FALSE.
seg_width: Controls the width of the segments if seg_plot = TRUE.
add_stat: Boolean parameter, set to TRUE to add regression lines, p value for each regression. Default is FALSE.
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).
plot_title: Required parameter, if out_path is specified. plot title, will also be pasted to the exported file.
return_data: Boolean parameter, set to TRUE and return the formatted data used for plotting. Default is FALSE

Value

Nothing.

Details

This function takes predictions returned with classify_samples(), together with a score variable, subtype class and returns a point plot (grob) with ranked scores along the x axis and scores along the y axis. The returned plot will also color fill the points based on subtype classification.

Examples

#run classifier
sjodahl_classes = classify_samples(this_data = sjodahl_2017, 
                                   log_transform = FALSE, 
                                   adjust = TRUE, 
                                   impute = TRUE, 
                                   include_data = TRUE, 
                                   verbose = FALSE)

#Seg plot, all 5 classes                                   
plot_ranked_score(these_predictions = sjodahl_classes, 
                  this_score = "proliferation_score", 
                  subtype_class = "5_class", 
                  seg_plot = TRUE, 
                  seg_width = 1)
#> Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
#> ℹ Please use the `linewidth` argument instead.
#> ℹ The deprecated feature was likely used in the LundTaxR package.
#>   Please report the issue to the authors.


#Seg plot, all 7 classes
plot_ranked_score(these_predictions = sjodahl_classes, 
                  this_score = "proliferation_score", 
                  subtype_class = "7_class", 
                  seg_plot = TRUE, 
                  seg_width = 1)


#rank plot, proliferation score vs 5 class subtypes
plot_ranked_score(these_predictions = sjodahl_classes, 
                  this_score = "proliferation_score", 
                  subtype_class = "5_class")


#rank plot with statis added
plot_ranked_score(these_predictions = sjodahl_classes, 
                  this_score = "proliferation_score", 
                  subtype_class = "5_class",
                  add_stat = TRUE,
                  this_subtype = "GU")
#> `geom_smooth()` using formula = 'y ~ x'

                  
#return data
ranked_proliferation = plot_ranked_score(these_predictions = sjodahl_classes, 
                                         this_score = "proliferation_score", 
                                         return_data = TRUE,
                                         subtype_class = "7_class")
#> No plot generated, returning plot data instead...
#view data
head(ranked_proliferation)
#>   sample_id     score subtype rank
#> 1     1.CEL 0.7310869    UroA  139
#> 2     2.CEL 1.0419366     Mes  242
#> 3     3.CEL 0.4846604      GU   30
#> 4     4.CEL 0.6596973    UroA  103
#> 5     5.CEL 0.8079496    UroB  170
#> 6     6.CEL 0.9343730      GU  219