survival_digitize: Survival Digitization

In Pechli-Lab/SurvdigitizeR: Digitizing Survival Curves

Survival Digitization

Description

A wrapper for the digitizer end-to-end process.

Usage

survival_digitize(
  img_path,
  bg_lightness = 0.3,
  attempt_OCR = F,
  word_sensitivity = 30,
  num_curves,
  censoring = F,
  x_start,
  x_end,
  x_increment,
  y_start,
  y_end,
  y_increment,
  y_text_vertical,
  nr_neighbors = 20,
  enhance = F,
  impute_size = 0,
  line_censoring = F
)

Arguments

img_path	Location of the image file.
bg_lightness	A lightness threshold value between 0 and 1. Every pixel with lightness > bg_lightness is considered background and removed. Default value is 0.3.
attempt_OCR	Logical value indicating if Optical Character Recognition (OCR) should be attempted to remove words. Default value is FALSE.
word_sensitivity	Sensitivity for OCR word removal. Default value is 30.
num_curves	The number of curves in an image.
censoring	Logical value indicating if censoring is represented by black marks. Default value is TRUE.
x_start	Lowest X-axis label value.
x_end	Highest X-axis label value.
x_increment	Increment value for the X-axis ticks. Note: this should include increment between every tick, including minor ones.
y_start	Lowest Y-axis label.
y_end	Highest Y-axis label.
y_increment	Increment value for the Y-axis ticks. Note: this should include increment between every tick, including minor ones.
y_text_vertical	Boolean value indicating if the Y-axis labels are vertical (TRUE) or horizontal (FALSE).
nr_neighbors	Number of neighbors in k-nearest neighbors (knn) when grouping pixels by colors. Default value is 50.
enhance	Logical value indicating whether to convert HSL channels into the same scale. Default value is FALSE.
impute_size	Size parameter for imputation. It defines the number of time intervals for imputation.
line_censoring	Logical value indicating if line censoring removal should be attempted. Default value is FALSE.

Value

A dataframe with columns: 'id', 'times', 'St', and 'curve'.

Examples

## Not run: 
survival_digitize(
  img_path = here::here("OS.jpg"),
  bg_lightness = 0.1,
  attempt_OCR = FALSE,
  num_curves = 2,
  x_start = 0,
  x_end = 10,
  x_increment = 1,
  y_start = 0,
  y_end = 1,
  y_increment = 0.2,
  y_text_vertical = TRUE
)

## End(Not run)

Pechli-Lab/SurvdigitizeR documentation built on July 17, 2024, 8:01 a.m.