plot.BoneProfileR: Plot a bone section

In BoneProfileR: Tools to Study Bone Compactness

Plot a bone section

Description

Display a bone section.
type value can be:
Image plot: 'original', 'mineralized', 'unmineralized', 'section'
Original is the original image, mineralized is the mineral interpretation of the section, unmineralized is the unmineralized interpretation of the section, section is the interpretation of the section.
'colors' shows the histograms of pixel information with foreground and background colors if they are defined.
'3Dcolors' show the pixels colors in 3D
Global analysis: 'observations', 'model', 'observations+model'
Radial analysis: 'radial'
If angle is not null and a radial analysis exists, it will show the model for this angle.
'mcmc': It will show the posterior distribution of parameter

Usage

## S3 method for class 'BoneProfileR'
plot(
  x,
  message = NULL,
  type = "original",
  angle = NULL,
  show.centers = TRUE,
  show.colors = TRUE,
  show.grid = TRUE,
  analysis = 1,
  parameter.mcmc = "S",
  options.mcmc = list(),
  restorePar = TRUE,
  mar = NULL,
  angle.3D = 55,
  CI = "ML",
  radial.variable = "S",
  show.legend = TRUE,
  ...
)

Arguments

x	The bone image
message	The message to be displayed
type	The type of plot; see description
angle	Which angle model to show
show.centers	Should the centers be shown?
show.colors	Should the background and foreground colors be shown?
show.grid	Should the grid be shown?
analysis	Name or number of analysis to be plotted
parameter.mcmc	The posterior parameter to show for type = "mcmc"
options.mcmc	The option to plot type mcmc output
restorePar	If TRUE, restore the par parameter at the exit
mar	The margin for type being "model" or "observations"
angle.3D	The angle between x and y for 3Dcolors graph
CI	Which confidence interval should be plotted: MCMC or ML
radial.variable	Name of the radial variable to plot
show.legend	Should a legend be shown?
...	Not used

Details

plot.BoneProfileR displays a bone section

Value

Nothing

Author(s)

Marc Girondot [e-mail]

See Also

Other BoneProfileR: BP_AutoFit(), BP_ChooseBackground(), BP_ChooseCenter(), BP_ChooseForeground(), BP_DetectBackground(), BP_DetectCenters(), BP_DetectForeground(), BP_DuplicateAnalysis(), BP_EstimateCompactness(), BP_FitBayesianCompactness(), BP_FitMLCompactness(), BP_FitMLRadialCompactness(), BP_GetFittedParameters(), BP_ListAnalyses(), BP_LnLCompactness(), BP_OpenImage(), BP_Report(), Erinaceus_europaeus, summary.BoneProfileR()

Examples

## Not run: 
# Not run:
library(BoneProfileR)
 bone <- BP_OpenImage()
 # or 
 path_Hedgehog <- system.file("extdata", "Erinaceus_europaeus_fem_2-1_small.png", 
                             package = "BoneProfileR")
 bone <- BP_OpenImage(file=path_Hedgehog)
 bone <- BP_DetectBackground(bone=bone, analysis="logistic")
 bone <- BP_DetectForeground(bone=bone, analysis="logistic")
 plot(bone, type="colors")
 bone <- BP_DetectCenters(bone=bone, analysis="logistic")
 plot(bone, type="3Dcolors")
 bone <- BP_EstimateCompactness(bone, analysis="logistic", rotation.angle = 1)
 bone <- BP_FitMLCompactness(bone, analysis="logistic")
 plot(bone)
 # 
path_Hedgehog <- system.file("extdata", "Erinaceus_europaeus_fem_2-1_small.png", 
                             package = "BoneProfileR")
 bone <- BP_OpenImage(file=path_Hedgehog)
 bone <- BP_DetectBackground(bone=bone, analysis="logistic")
 bone <- BP_DetectForeground(bone=bone, analysis="logistic")
 bone <- BP_DetectCenters(bone=bone, analysis="logistic")
 bone <- BP_EstimateCompactness(bone, analysis="logistic")
 bone <- BP_FitMLCompactness(bone, analysis="logistic")
 plot(bone)
 plot(bone, type="observations")
 plot(bone, type="observations+model", analysis=1)
 bone <- BP_DuplicateAnalysis(bone, from="logistic", to="flexit")
 fittedpar <- BP_GetFittedParameters(bone, analysis="logistic")
 bone <- BP_DuplicateAnalysis(bone, from="logistic", to="flexit")
 bone <- BP_FitMLCompactness(bone, 
                fitted.parameters=c(fittedpar, K1=1, K2=1), 
                fixed.parameters=NULL, analysis="flexit")
 compare_AIC(Logistic=BP_GetFittedParameters(bone, analysis="logistic", alloptim=TRUE), 
             Flexit=BP_GetFittedParameters(bone, analysis="flexit", alloptim=TRUE))
 out4p <- plot(bone, type="observations+model", analysis="logistic")
 out6p <- plot(bone, type="observations+model", analysis="flexit")
 bone <- BP_FitBayesianCompactness(bone, analysis="logistic")
 plot(bone, type="observations+model", CI="MCMC")
 bone <- BP_FitMLRadialCompactness(bone)
 plot(bone, type="radial", radial.variable=c("P", "S"))
 plot(bone, type="radial", radial.variable=c("P", "S", "Min", "Max"))

## End(Not run)

BoneProfileR documentation built on Sept. 11, 2024, 6:07 p.m.