| Type: | Package |
| Title: | Visualize and Parse the Output of 'BeXY' |
| Version: | 0.1.3 |
| Maintainer: | Madleina Caduff <madleina.caduff@unifr.ch> |
| Description: | Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (https://bitbucket.org/wegmannlab/bexy), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data. |
| License: | GPL-2 |
| Encoding: | UTF-8 |
| Imports: | TeachingDemos,Ternary |
| RoxygenNote: | 7.3.1 |
| NeedsCompilation: | no |
| Packaged: | 2024-08-23 13:08:09 UTC; madleina |
| Author: | Madleina Caduff [aut, cre], Raphael Eckel [ctb], Christoph Leuenberger [ctb], Daniel Wegmann [aut] |
| Repository: | CRAN |
| Date/Publication: | 2024-08-23 13:30:02 UTC |
Function to create a legend
Description
Function to create a legend
Usage
.addLegend.bexy(x_coord, y_coord, colors)
Arguments
x_coord |
The x-coordinate for legend. |
y_coord |
The y-coordinate for legend. |
colors |
A vector of length three with the colors for aneuploid, XX and XY samples, respectively. |
Value
No return value, called for side effects.
Function to create a legend for autosomal trisomy
Description
Function to create a legend for autosomal trisomy
Usage
.addLegendAutosomalTrisomy.bexy(x_coord, y_coord, scaffoldName, colors)
Arguments
x_coord |
The x-coordinate for legend. |
y_coord |
The y-coordinate for legend. |
scaffoldName |
The name of the scaffold to plot (has to be an autosome). |
colors |
A vector of length two with the colors for triploid and diploid samples, respectively. |
Value
No return value, called for side effects.
Function that returns all possible autosomal trisomy states used in BeXY
Description
Function that returns all possible autosomal trisomy states used in BeXY
Usage
.getAllPossibleAutosomalTrisomy.bexy(scaffoldName)
Arguments
scaffoldName |
A vector of size one with the name of a scaffold. |
Value
A vector of characters.
Function that returns all possible scaffold types used in BeXY
Description
Function that returns all possible scaffold types used in BeXY
Usage
.getAllPossibleScaffoldTypes.bexy()
Value
A vector of characters.
Function that returns all possible sex karyotypes used in BeXY
Description
Function that returns all possible sex karyotypes used in BeXY
Usage
.getAllPossibleSexKaryotypes.bexy()
Value
A vector of characters.
Function to extract specific columns from a data frame or matrix
Description
Function to extract specific columns from a data frame or matrix
Usage
.getColumns.bexy(what, name)
Arguments
what |
A matrix or data frame |
name |
The name of the parameter to extract. |
Value
A subset of the matrix or data frame containing only the columns whose names match the argument 'name'
Function that returns the index of a given scaffold
Description
Function that returns the index of a given scaffold
Usage
.getIndexScaffold.bexy(object, scaffoldName, takeIfNotFound)
Arguments
object |
A bexy object. |
scaffoldName |
A string representing the name of a scaffold. |
takeIfNotFound |
A string ("X-linked" or "Y-linked") that denotes the type of scaffold to use if scaffoldName could not be found |
Value
A single integer representing the index of the scaffold.
Function that returns the index of a given scaffold & checks if it is valid for autosomal trisomy
Description
Function that returns the index of a given scaffold & checks if it is valid for autosomal trisomy
Usage
.getIndexScaffoldAutosomalTrisomy.bexy(object, scaffoldName)
Arguments
object |
A bexy object. |
scaffoldName |
A vector of size one with the name of a scaffold. |
Value
A list containing the index of the scaffold within posterior_mode_z and counts.
Function that transforms state posteriors of sex karyotype to ternary-format
Description
Function that transforms state posteriors of sex karyotype to ternary-format
Usage
.getInputTernary.bexy(object)
Arguments
object |
A bexy object. |
Value
A matrix with 3 rows: P(aneuploid), P(XX), P(XY).
Function to select samples that should be highlighted
Description
Function to select samples that should be highlighted
Usage
.getSamplesToHighlight.bexy(object, sampleNamesToHighlight)
Arguments
object |
A bexy object. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
Value
A vector of integers corresponding to indices of samples to highlight
Function to select samples that should be highlighted for autosomal trisomy
Description
Function to select samples that should be highlighted for autosomal trisomy
Usage
.getSamplesToHighlightAutosomalTrisomy.bexy(object, ix, sampleNamesToHighlight)
Arguments
object |
A bexy object. |
ix |
A list containing the index of a specific scaffold within z. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
Value
A vector of integers corresponding to indices of samples to highlight
Function that returns the scaffold names of z
Description
Function that returns the scaffold names of z
Usage
.getScaffoldNames.bexy(names_z, numSamples)
Arguments
names_z |
A character vector with the column names of z |
numSamples |
The number of samples |
Value
A vector of characters.
Function to get the width of a string on the current plotting device in user coordinates
Description
Function to get the width of a string on the current plotting device in user coordinates
Usage
.getStringWidth.bexy(name)
Arguments
name |
A string. |
Value
The width of the input string on the current plotting device in user coordinates.
Function to open a file and generate error message if it was not found
Description
Function to open a file and generate error message if it was not found
Usage
.openFile.bexy(path, files, patterns)
Arguments
path |
A file path. |
files |
A vector of character strings corresponding to file names found in the path. |
patterns |
A vector of patterns to search for within 'files'. |
Value
A file connection.
Function to plot counts of a specific autosome and color them according to BeXY posterior mode of autosomal trisomy
Description
Function to plot counts of a specific autosome and color them according to BeXY posterior mode of autosomal trisomy
Usage
.plotAutosomalTrisomy.bexy(
object,
scaffoldName,
plotCounts,
colors,
sampleNamesToHighlight,
label,
...
)
Arguments
object |
A bexy object. |
scaffoldName |
The name of the scaffold to plot (has to be an autosome) |
plotCounts |
A boolean. If TRUE, the counts are plotted. If FALSE, the posterior probabilities are plotted. |
colors |
A vector of length two with the colors for diploid and triploid samples, respectively. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
label |
Boolean indicating whether samples should be labeled. |
... |
Other parameters used for plotting |
Value
No return value, called for side effects.
Function to plot a ternary plot of the probabilities for being aneuploid, XX or XY
Description
Function to plot a ternary plot of the probabilities for being aneuploid, XX or XY
Usage
.plotTernary.bexy(object, colors, sampleNamesToHighlight, label, ...)
Arguments
object |
A bexy object. |
colors |
A vector of length three with the colors for aneuploid, XX and XY samples, respectively. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
label |
Boolean indicating whether samples should be labeled. |
... |
More parameters passed to TernaryPlot() |
Value
The upper boundary of the plot.
Function to plot ternary plot with 7-cell plots displaying posterior probabilities of karyotypes
Description
Function to plot ternary plot with 7-cell plots displaying posterior probabilities of karyotypes
Usage
.plotTernaryAndTicTacToe.bexy(
object,
colors,
sampleNamesToHighlight,
label,
addSquares,
...
)
Arguments
object |
A bexy object. |
colors |
A vector of length three with the colors for aneuploid, XX and XY samples, respectively. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
label |
Boolean indicating whether samples should be labeled. |
addSquares |
Boolean indicating whether 7-cell posterior probability square plots should be drawn. |
... |
Other parameters used for plotting |
Value
No return value, called for side effects.
Function to plot a single 7-cell plot displaying posterior probabilities of karyotypes
Description
Function to plot a single 7-cell plot displaying posterior probabilities of karyotypes
Usage
.plotTicTacToeWithCoordinates.bexy(
object,
ix,
label,
x_coords,
y_coords,
last,
colors
)
Arguments
object |
A bexy object. |
ix |
The sample index. |
label |
The sample name used as a label. |
x_coords |
Left and right x-coordinates for 7-cell plot. |
y_coords |
Bottom and top y-coordinates for 7-cell plot. |
last |
Boolean indicating if this is the last sample to be plotted. |
colors |
A vector of length three with the colors for aneuploid, XX and XY samples, respectively. |
Value
No return value, called for side effects.
Function to plot X vs Y counts and color them according to BeXY posterior mode
Description
Function to plot X vs Y counts and color them according to BeXY posterior mode
Usage
.plotXVsY.bexy(object, ix_X, ix_Y, colors, sampleNamesToHighlight, label, ...)
Arguments
object |
A bexy object. |
ix_X |
An integer representing the index of the scaffold to be plotted on the x-axis. |
ix_Y |
An integer representing the index of the scaffold to be plotted on the y-axis. |
colors |
A vector of length three with the colors for aneuploid, XX and XY samples, respectively. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
label |
Boolean indicating whether samples should be labeled. |
... |
Other parameters used for plotting |
Value
No return value, called for side effects.
Function to reformat column names
Description
Function to reformat column names
Usage
.renameHeader.bexy(file, pattern)
Arguments
file |
A file whose header should be renamed. |
pattern |
Where to split. |
Value
A new file with re-formatted column names.
Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data
Description
Visualization of results produced by BeXY
Usage
bexy(path = NULL, readMCMCTrace = FALSE)
Arguments
path |
The path where all the output files of BeXY are located. If NULL, the example files will be loaded. |
readMCMCTrace |
If TRUE, read the full trace of the MCMC of all parameters (potentially slow). |
Value
An object of type bexy.
Getting posterior mean rho (ploidy ratio parameter) for each scaffold
Description
Getting posterior mean rho (ploidy ratio parameter) for each scaffold
Usage
getPosteriorMeanRho(object)
Arguments
object |
A bexy object. |
Value
A numeric vector containing the posterior mean of rho for each scaffold
See Also
Examples
bex <- bexy()
getPosteriorMeanRho(bex)
Getting the posterior mode for each autosomal trisomy
Description
Getting the posterior mode for each autosomal trisomy
Usage
getPosteriorModeAutosomalTrisomy(
object,
scaffoldName,
threshold_certainty = 0.9
)
Arguments
object |
A bexy object. |
scaffoldName |
The scaffold name, must be an autosome. |
threshold_certainty |
The threshold for certainty on the posterior probabilities. All samples that have a posterior probability less than this threshold are classified as 'uncertain'. |
Value
A character vector containing the trisomy classification for each sample for the given scaffold
See Also
Examples
bex <- bexy()
getPosteriorModeAutosomalTrisomy(bex, "21")
Getting the posterior mode for each scaffold type
Description
Getting the posterior mode for each scaffold type
Usage
getPosteriorModeScaffoldTypes(object, threshold_certainty = 0.9)
Arguments
object |
A bexy object. |
threshold_certainty |
The threshold for certainty on the posterior probabilities. All scaffolds that have a posterior probability less than this threshold are classified as 'uncertain'. |
Value
A character vector containing the scaffold type classification for each scaffold
See Also
Examples
bex <- bexy()
getPosteriorModeScaffoldTypes(bex)
Getting the posterior mode for each sex karyotype
Description
Getting the posterior mode for each sex karyotype
Usage
getPosteriorModeSexKaryotypes(object, threshold_certainty = 0.9)
Arguments
object |
A bexy object. |
threshold_certainty |
The threshold for certainty on the posterior probabilities. All samples that have a posterior probability less than this threshold are classified as 'uncertain'. |
Value
A character vector containing the sex karyotype classification for each sample
See Also
Examples
bex <- bexy()
getPosteriorModeSexKaryotypes(bex)
Getting all samples classified as a certain autosomal trisomy
Description
Getting all samples classified as a certain autosomal trisomy
Usage
getSamplesWithAutosomalTrisomy(object, scaffoldName, threshold_certainty = 0.9)
Arguments
object |
A bexy object. |
scaffoldName |
The scaffold name, must be an autosome. |
threshold_certainty |
The threshold for certainty on the posterior probabilities. All samples that have a posterior probability less than this threshold are classified as 'uncertain'. |
Value
A character vector containing all sample names that are classified as having an autosomal trisomy of scaffold 'scaffoldName'
See Also
Examples
bex <- bexy()
getSamplesWithAutosomalTrisomy(bex, "21")
Getting all samples classified as a specific sex karyotype
Description
Getting all samples classified as a specific sex karyotype
Usage
getSamplesWithThisKaryotype(object, karyotype, threshold_certainty = 0.9)
Arguments
object |
A bexy object. |
karyotype |
One specific sex karyotype, can be XY, XX, X0, XXY, XYY, XXX or XXYY. |
threshold_certainty |
The threshold for certainty on the posterior probabilities. All samples that have a posterior probability less than this threshold are classified as 'uncertain'. |
Value
A character vector containing all sample names that are classified as the sex karyotype given by argument 'karyotype'.
See Also
Examples
bex <- bexy()
getSamplesWithThisKaryotype(bex, "XX")
Getting all scaffolds classified as a specific scaffold type
Description
Getting all scaffolds classified as a specific scaffold type
Usage
getScaffoldsWithThisType(object, type, threshold_certainty = 0.9)
Arguments
object |
A bexy object. |
type |
One specific scaffold type, can be Autosome, Y-linked, X-linked or Different. |
threshold_certainty |
The threshold for certainty on the posterior probabilities. All scaffolds that have a posterior probability less than this threshold are classified as 'uncertain'. |
Value
A character vector containing all scaffold names that are classified as the scaffold type given by argument 'type'.
See Also
Examples
bex <- bexy()
getScaffoldsWithThisType(bex, "X-linked")
Plotting a bexy object. To customize the plots, please call the respective plotting functions directly (e.g. plotTernary, plotCounts, plotBars...).
Description
Plotting a bexy object. To customize the plots, please call the respective plotting functions directly (e.g. plotTernary, plotCounts, plotBars...).
Usage
## S3 method for class 'bexy'
plot(x, ...)
Arguments
x |
A bexy object. |
... |
Other parameters used for plotting. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
plot(bex)
Plotting the autosomal trisomies
Description
Plotting the autosomal trisomies
Usage
plotAutosomalTrisomy(
x,
scaffoldName,
colors = c("deepskyblue4", "darkred"),
sampleNamesToHighlight = c(),
label = TRUE,
...
)
Arguments
x |
A bexy object. |
scaffoldName |
The name of the scaffold to plot (has to be an autosome) |
colors |
A vector of length two with the colors for diploid and triploid samples, respectively. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
label |
Boolean indicating whether samples should be labeled. |
... |
Other parameters used for plotting. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
plotAutosomalTrisomy(bex, "21")
Plotting the autosomal trisomies: counts on that scaffold
Description
Plotting the autosomal trisomies: counts on that scaffold
Usage
plotAutosomalTrisomyCounts(
x,
scaffoldName,
colors = c("deepskyblue4", "darkred"),
sampleNamesToHighlight = c(),
label = TRUE,
...
)
Arguments
x |
A bexy object. |
scaffoldName |
The name of the scaffold to plot (has to be an autosome) |
colors |
A vector of length two with the colors for diploid and triploid samples, respectively. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
label |
Boolean indicating whether samples should be labeled. |
... |
Other parameters used for plotting. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
plotAutosomalTrisomyCounts(bex, "21")
Plotting the autosomal trisomies: posterior probabilities
Description
Plotting the autosomal trisomies: posterior probabilities
Usage
plotAutosomalTrisomyPosteriorProbabilities(
x,
scaffoldName,
colors = c("deepskyblue4", "darkred"),
sampleNamesToHighlight = c(),
label = TRUE,
...
)
Arguments
x |
A bexy object. |
scaffoldName |
The name of the scaffold to plot (has to be an autosome) |
colors |
A vector of length two with the colors for diploid and triploid samples, respectively. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
label |
Boolean indicating whether samples should be labeled. |
... |
Other parameters used for plotting. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
plotAutosomalTrisomyPosteriorProbabilities(bex, "21")
Plotting a barplot with the posterior probabilities of each sex karyotype per sample
Description
Plotting a barplot with the posterior probabilities of each sex karyotype per sample
Usage
plotBars(
x,
colors = c("lightblue", "lightpink", "khaki", "maroon1", "dodgerblue3", "red4", "navy"),
maxNumSamplesPerPlot = 100,
sortByKaryotype = TRUE,
sampleNames = c(),
...
)
Arguments
x |
A bexy object. |
colors |
A vector of length 7 with the colors for XY, XX, X0, XXY, XYY, XXX and XXYY, respectively. |
maxNumSamplesPerPlot |
How many samples to place next to each other into one barplot. If there are more samples, multiple barplots will be generated. This is to ensure that the labels are readable. |
sortByKaryotype |
If TRUE, the samples (i.e. the bars) are ordered by the posterior mode of the sex karyotype. |
sampleNames |
A vector of sample names that represents the order in which the bars are plotted. Overrides any argument given to sortByKaryotype. |
... |
Other parameters used for plotting. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
plotBars(bex)
Plotting the percentage of counts mapping to two scaffolds (by default a Y-linked scaffold against a X-linked scaffold), colored by sex karyotype
Description
Plotting the percentage of counts mapping to two scaffolds (by default a Y-linked scaffold against a X-linked scaffold), colored by sex karyotype
Usage
plotCounts(
x,
scaffoldX = NULL,
scaffoldY = NULL,
colors = c("turquoise3", "darkorange", "royalblue4"),
sampleNamesToHighlight = c(),
label = TRUE,
...
)
Arguments
x |
A bexy object. |
scaffoldX |
A string with the name of the scaffold to be plotted on the x-axis. If NULL (default), a X-linked scaffold is used. |
scaffoldY |
A string with the name of the scaffold to be plotted on the y-axis. If NULL (default), a Y-linked scaffold is used. |
colors |
A vector of length three with the colors for aneuploid, XX and XY samples, respectively. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
label |
Boolean indicating whether samples should be labeled. |
... |
Other parameters used for plotting. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
plotCounts(bex)
Plot the MCMC trace for a specific parameter
Description
Plot the MCMC trace for a specific parameter
Usage
plotMCMCTrace(object, parameterName, maxNumPlots = 20)
Arguments
object |
A bexy object. |
parameterName |
The name of the parameter to plot (e.g. rho, logSigma, epsilon, s, t, a, f, ...) |
maxNumPlots |
The maximum number of plots to plot, default 20. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy(readMCMCTrace = TRUE)
plotMCMCTrace(bex, "rho", maxNumPlots = 1)
Plotting the ternary of a bexy object
Description
Plotting the ternary of a bexy object
Usage
plotTernary(
x,
colors = c("turquoise3", "darkorange", "royalblue4"),
sampleNamesToHighlight = c(),
label = TRUE,
addSquares = TRUE,
...
)
Arguments
x |
A bexy object. |
colors |
A vector of length three with the colors for aneuploid, XX and XY samples, respectively. |
sampleNamesToHighlight |
A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities. |
label |
Boolean indicating whether samples should be labeled. |
addSquares |
Boolean indicating whether 7-cell posterior probability square plots should be drawn. |
... |
Other parameters used for plotting. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
plotTernary(bex)
Printing a bexy object
Description
Printing a bexy object
Usage
## S3 method for class 'bexy'
print(x, ...)
Arguments
x |
A bexy object. |
... |
Additional parameters passed to print functions. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
print(bex)
Summarizing a bexy object
Description
Summarizing a bexy object
Usage
## S3 method for class 'bexy'
summary(object, ...)
Arguments
object |
A bexy object. |
... |
Additional parameters passed to summary functions. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
print(bex)
Write a file with the posterior mode for each autosomal trisomy
Description
Write a file with the posterior mode for each autosomal trisomy
Usage
writePosteriorModeAutosomalTrisomies(
object,
scaffoldName,
file,
threshold_certainty = 0.9
)
Arguments
object |
A bexy object. |
scaffoldName |
The scaffold name, must be an autosome. |
file |
The name of the output file. |
threshold_certainty |
The threshold for certainty on the posterior probabilities. All samples that have a posterior probability less than this threshold are classified as 'uncertain'. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
tf <- tempfile(fileext = ".txt")
writePosteriorModeAutosomalTrisomies(bex, "21", tf)
Write a file with the posterior mode for each scaffold type
Description
Write a file with the posterior mode for each scaffold type
Usage
writePosteriorModeScaffoldTypes(object, file, threshold_certainty = 0.9)
Arguments
object |
A bexy object. |
file |
The name of the output file. |
threshold_certainty |
The threshold for certainty on the posterior probabilities. All scaffolds that have a posterior probability less than this threshold are classified as 'uncertain'. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
tf <- tempfile(fileext = ".txt")
writePosteriorModeScaffoldTypes(bex, tf)
Write a file with the posterior mode for each sex karyotype
Description
Write a file with the posterior mode for each sex karyotype
Usage
writePosteriorModeSexKaryotypes(object, file, threshold_certainty = 0.9)
Arguments
object |
A bexy object. |
file |
The name of the output file. |
threshold_certainty |
The threshold for certainty on the posterior probabilities. All samples that have a posterior probability less than this threshold are classified as 'uncertain'. |
Value
No return value, called for side effects.
See Also
Examples
bex <- bexy()
tf <- tempfile(fileext = ".txt")
writePosteriorModeSexKaryotypes(bex, tf)