| Version: | 1.0.3 |
| Title: | Visualization Tools for Genealogical Data |
| Description: | Methods for searching through genealogical data and displaying the results. Plotting algorithms assist with data exploration and publication-quality image generation. Includes interactive genealogy visualization tools. Provides parsing and calculation methods for variables in descendant branches of interest. Uses the Grammar of Graphics. |
| Author: | Lindsay Rutter, Susan Vanderplas, Di Cook |
| Maintainer: | Lindsay Rutter <ggenealogypackage@gmail.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL] |
| Depends: | R (≥ 3.6.0) |
| Imports: | ggplot2 (≥ 2.2.0), igraph (≥ 0.7.1), plyr (≥ 1.8.1), reshape2 (≥ 1.4), plotly (≥ 4.5.6) |
| VignetteBuilder: | knitr |
| Suggests: | stringr (≥ 0.6.2), knitr (≥ 1.13), roxygen2 (≥ 3.0.0), dplyr (≥ 0.5.0) |
| RoxygenNote: | 7.2.3 |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| Packaged: | 2024-02-21 15:39:35 UTC; suzu |
| Repository: | CRAN |
| Date/Publication: | 2024-02-21 16:00:02 UTC |
Returns the coordinate positions of all ancestors and descendants of a variety.
Description
Calculates coordinates to plot each ancestors and descendant of a variety in a lineage. The x and y values describe the coordinates of the label, while the xstart, ystart, xend, and yend values describe the edges of the label.
Usage
buildAncDesCoordDF(df)
Arguments
df |
the data frame of the ancestors and descendants of a variety (from function buildAncDesTotalDF) |
References
See Also
buildAncList for information on determining ancestors
buildDesList for information on determining descendants
Returns data frame with plot coordinates of all ancestors and descendants of a variety.
Description
Returns the data frame that includes labels and plot coordinates of all ancestors and descendants of a variety. Users can specify the maximum number of ancestors and descendants to display.
Usage
buildAncDesTotalDF(v1, geneal, mAnc = 3, mDes = 3)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
mAnc |
the maximum number of generations of ancestors of v1 to be displayed (in numeric format) |
mDes |
the maximum number of generations of descendants of v1 to be displayed (in numeric format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
See Also
buildAncList for information on determining ancestors
buildDesList for information on determining descendants
Examples
data(sbGeneal)
v1 <- "Essex"
buildAncDesTotalDF(v1, sbGeneal)
Returns the ancestors of a particular variety (if they exist).
Description
This function returns a nested list of the ancestors of the inputted variety.
Usage
buildAncList(v1, geneal, gen = 0)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
gen |
the generation (note: This should be left as default, as any other input will not affect results anyway) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
See Also
getParent for information on determining parents
Examples
data(sbGeneal)
getParent("Essex", sbGeneal)
buildAncList("Essex", sbGeneal)
Returns the descendants of a particular variety (if they exist).
Description
This function returns a nested list of the descendants of the inputted variety.
Usage
buildDesList(v1, geneal, gen = 0)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
gen |
the generation (note: This should be left as default, as any other input will not affect results) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
See Also
getChild for information on determining children
Examples
data(sbGeneal)
getParent("Essex", sbGeneal)
buildDesList("Essex", sbGeneal, 3)
Build the edges in the genealogy graph.
Description
This function takes the graph object and creates a data frame object of the edges between all parent-child relationships in the graph.
Usage
buildEdgeTotalDF(geneal, ig, colName, bin = 12)
Arguments
geneal |
the full genealogy (in data frame format) |
ig |
the graph representation of the data genealogy (in igraph format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
bin |
the number of bins to determine the vertical positions of nodes (default is 12). For more information on choosing bin size, please visit the ggenealogy vignette. |
See Also
dfToIG for information on producing ig from the genealogy
https://www.r-project.org for iGraph information
Process the genealogy graph
Description
This function takes the spreadTotalDF object (from the buildSpreadTotalDF function) and the path object as inputs. From these objects, it creates a data frame object of the label, x, and y values of all nodes in the ful genealogy. However, the data frame object does not include the labels of the path varieties, as they will be treated differently.
Usage
buildMinusPathDF(path, geneal, ig, colName, colNameY, bin = 12)
Arguments
path |
path as returned from getPath() or a vector of two variety names which exist in the ig object |
geneal |
the full genealogy (in data frame format) |
ig |
the graph representation of the data genealogy (in igraph format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
colNameY |
the name of the second optional column of the data frame that contains the second optional quantitative variable of interest (in character string format). This optional quantitative variable will be plotted on the vertical axis. |
bin |
the number of bins to determine the vertical positions of nodes (default is 12). For more information on choosing bin size, please visit the ggenealogy vignette. |
See Also
https://www.r-project.org for iGraph information
getPath for information on input path building
Build data frame for path representation
Description
This function builds a dataframe of information about the path object that can later be used for visualization. The dataframe includes "label" (name of each variety) of each node, "x" (the date of the variety, the x-axis value for which the label and incoming/outgoing edges are centered), "y" (the y-axis value, which is the index of the path, incremented by unity), "xstart" (the x-axis position of the outgoing edge (leaving to connect to the node at the next largest y-value)), "xend" (the x-axis position of the outgoing edge (connected to the node at the next largest y-value)), "ystart" (the y-axis position of the outgoing edge (leaving to connect to the node at the next largest y-value), "yend" (the y-axis position of the outgoing edge (connected to the node at the next largest y-value))).
Usage
buildPathDF(path, geneal, colName, colNameY = "")
Arguments
path |
path object representing the path between two vertices |
geneal |
the full genealogy (in data frame format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
colNameY |
the name of the second optional column of the data frame that contains the second optional quantitative variable of interest (in character string format). This optional quantitative variable will be plotted on the vertical axis. |
Build all labels in the graph
Description
This function takes the spreadTotalDF object (from the buildSpreadTotalDF function) and the path object as inputs. From these objects, it creates a data frame object of the text label positions for the varieties in the path, as well as the edges only in the varieties in the path.
Usage
buildPlotTotalDF(path, geneal, ig, colName, colNameY = "", bin = 12)
Arguments
path |
path as returned from getPath() or a vector of two variety names which exist in ig |
geneal |
the full genealogy (in data frame format) |
ig |
the graph representation of the data genealogy (in igraph format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
colNameY |
the name of the second optional column of the data frame that contains the second optional quantitative variable of interest (in character string format). This optional quantitative variable will be plotted on the vertical axis. |
bin |
the number of bins to determine the vertical positions of nodes (default is 12). For more information on choosing bin size, please visit the ggenealogy vignette |
See Also
https://www.r-project.org for iGraph information
https://www.r-project.org for iGraph information
getPath for information on input path building
Build a data frame where the varieties are spread so they do not overlap
Description
Constructs a data frame object so that varieties are spread such that they do not overlap, even though the x-axis position will represent dates.
Usage
buildSpreadTotalDF(geneal, ig, colName, bin = 12)
Arguments
geneal |
the full genealogy (in data frame format) |
ig |
the graph representation of the data genealogy (in igraph format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
bin |
the number of bins to determine the vertical positions of nodes (default is 12). For more information on choosing bin size, please visit the ggenealogy vignette |
See Also
https://www.r-project.org for iGraph information
Process the genealogy graph
Description
Processes the genealogy into an igraph object with appropriate vertex information, graph type, and edge weights.
Usage
dfToIG(geneal, vertexinfo = NULL, edgeweights = 1, isDirected = FALSE)
Arguments
geneal |
the full genealogy (in data frame format) |
vertexinfo |
(default NULL) either names of columns in the genealogy which should be added to the database as vertex information or a data frame with information for all vertices such that the first column contains vertex names. |
edgeweights |
(default 1) name of a column which contains edge weights |
isDirected |
(default FALSE) should the graph be a directed graph? |
See Also
https://www.r-project.org for iGraph information
Returns a list of the ancestors of a particular variety (if they exist)
Description
This function returns a list of the ancestors of the inputted variety within and including a given number of generations
Usage
getAncestors(v1, geneal, gen = 3)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
gen |
the number of generations back to include as ancestors |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
getParent("Essex", sbGeneal)
getAncestors("Essex", sbGeneal, 1)
getAncestors("Essex", sbGeneal, 5)
Determine basic statistics of the graph object
Description
Returns basic statistics of the graph object (number of nodes, number of edges, whether or not the whole graph is connected, number of components, average path length, graph diameter, etc.)
Usage
getBasicStatistics(ig)
Arguments
ig |
the graph representation of the data genealogy (in igraph format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
ig <- dfToIG(sbGeneal)
getBasicStatistics(ig)
Descendant branch calculations for quantitative variable
Description
Returns a data frame containing the names of all children of an individual of interest ("Name"). The mean and standard deviation ("Mean" and "SD") of a quantitative variable across all descendents of each child is reported. In addition, for each child, the number of its descendants is reported ("Count"), the number of its descendants who do not have a value for the quantitative variable ("NACount") is reported, and the names of all of its descendants is reported ("DesNames").
Usage
getBranchQual(v1, geneal, colName, rExpr, gen = 3)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
colName |
the name of the column of the data frame that contains the qualitative variable of interest (in character string format) |
rExpr |
regular expression to be applied to the column that contains the qualitative variable of interest (in character string format). The regular expression syntax must work on a data frame column of type character. The term geneal$colName must be used in the regular expression. |
gen |
the number of generations back to include as ancestors |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(statGeneal)
rExpr = "geneal$colName=='The Johns Hopkins University'"
DC_JHU = getBranchQual("David Cox", statGeneal, "school", rExpr, 15)
rExpr = "geneal$colName=='UnitedKingdom'"
DC_UK = getBranchQual("David Cox", statGeneal, "country", rExpr, 15)
rExpr = "grepl('(?i)Stochastic', geneal$colName)"
DC_Stochastic = getBranchQual("David Cox", statGeneal, "thesis", rExpr, 15)
Descendant branch calculations for quantitative variable
Description
Returns a data frame containing the names of all children of an individual of interest ("Name"). The mean and standard deviation ("Mean" and "SD") of a quantitative variable across all descendents of each child is reported. In addition, for each child, the number of its descendants is reported ("Count"), the number of its descendants who do not have a value for the quantitative variable ("NACount") is reported, and the names of all of its descendants is reported ("DesNames").
Usage
getBranchQuant(v1, geneal, colName, gen = 3)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
gen |
the number of generations back to include as ancestors |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(statGeneal)
DC_Year <- getBranchQuant("David Cox", statGeneal, "gradYear", 15)
Returns the children of a particular variety (if they exist)
Description
This function returns zero or more values that indicate the children of the inputted variety.
Usage
getChild(v1, geneal)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
getChild("Tokyo", sbGeneal)
getChild("Essex", sbGeneal)
Determine the degree between two varieties
Description
Returns the degree (distance between unweighted edges) between two varieties, where an edge represents a parent-child relationship
Usage
getDegree(v1, v2, ig, geneal)
Arguments
v1 |
the label of the first vertex of interest (in character string format) |
v2 |
the label of the second vertex of interest (in character string format) |
ig |
the graph representation of the data genealogy (in igraph format) |
geneal |
the full genealogy (in data frame format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
ig <- dfToIG(sbGeneal)
getDegree("Brim", "Bedford", ig, sbGeneal)
Returns a list of the descendants of a particular variety (if they exist)
Description
This function returns a list of the descendants of the inputted variety within and including a given number of generations
Usage
getDescendants(v1, geneal, gen = 3)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
gen |
the number of generations back to include as descendants |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
getChild("Essex", sbGeneal)
getDescendants("Essex", sbGeneal, 1)
getDescendants("Essex", sbGeneal, 3)
Returns edges (vertex names and edge weights) for the full genealogy
Description
Returns a matrix, where each row contains information about an edge (two vertex names and edge weight, if present) of the full genealogy.
Usage
getEdges(ig, geneal)
Arguments
ig |
the graph representation of the data genealogy (in igraph format) |
geneal |
the full genealogy (in data frame format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
ig <- dfToIG(sbGeneal)
getEdges(ig, sbGeneal)
Returns the nodes for a full genealogy
Description
Returns a character list, where rows contains names of the unique nodes in the full genealogy
Usage
getNodes(geneal)
Arguments
geneal |
the full genealogy (in data frame format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
getNodes(sbGeneal)
Returns the parents of a particular variety (if they exist)
Description
This function returns up to two values that indicate the parents of the inputted variety.
Usage
getParent(v1, geneal)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
getParent("Tokyo", sbGeneal)
getParent("Essex", sbGeneal)
Determine the path between two varieties
Description
Determines the shortest path between the two inputted vertices, and takes into account whether or not the graph is directed. If there is a path, the list of vertices of the path will be returned. If there is not a path, a list of character(0) will be returned. Note: For a directed graph, the direction matters. However, this function will check both directions and return the path if it exists.
Usage
getPath(v1, v2, ig, geneal, colName, silent = FALSE, isDirected = FALSE)
Arguments
v1 |
the label of the first vertex of interest (in character string format) |
v2 |
the label of the second vertex of interest (in character string format) |
ig |
the graph representation of the data genealogy (in igraph format) |
geneal |
the full genealogy (in data frame format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
silent |
whether or not to print output (defaults to false) |
isDirected |
whether or not the graph is directed (defaults to false) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
ig <- dfToIG(sbGeneal)
getPath("Brim", "Bedford", ig, sbGeneal, "devYear")
getPath("Tokyo", "Volstate", ig, sbGeneal, "yield")
Determine the path between two varieties
Description
Determines the shortest path between the two inputted vertices, and takes into account whether or not the graph is directed. If there is a path, the list of vertices of the path will be returned. If there is not a path, a list of character(0) will be returned. Note: For a directed graph, the direction matters. However, this function will check both directions and return the path if it exists.
Usage
getPathOnly(v1, v2, ig, geneal, silent = FALSE, isDirected = FALSE)
Arguments
v1 |
the label of the first vertex of interest (in character string format) |
v2 |
the label of the second vertex of interest (in character string format) |
ig |
the graph representation of the data genealogy (in igraph format) |
geneal |
the full genealogy (in data frame format) |
silent |
whether or not to print output (defaults to false) |
isDirected |
whether or not the graph is directed (defaults to false) |
Determine the date of a variety
Description
Returns the documented date of the inputted variety
Usage
getVariable(v1, geneal, colName)
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
getVariable("Essex", sbGeneal, "devYear")
getVariable("Tokyo", sbGeneal, "yield")
Determine if a variety is a child of another
Description
Returns a boolean variable for whether the first variety is a child of the second variety
Usage
isChild(child, parent, geneal)
Arguments
child |
possible child variety |
parent |
possible parent variety |
geneal |
the full genealogy (in data frame format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
isChild("Essex", "Young", sbGeneal)
isChild("Young", "Essex", sbGeneal)
Determine if a variety is a parent of another
Description
Returns a boolean variable for whether the second variety is a parent of the first variety
Usage
isParent(child, parent, geneal)
Arguments
child |
possible child variety |
parent |
possible parent variety |
geneal |
the full genealogy (in data frame format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
isParent("Essex", "Young", sbGeneal)
isParent("Young", "Essex", sbGeneal)
Returns the data frame representation of all ancestors and descendants of a variety
Description
Converts the list-style-genealogy to a data frame, where each variety has an id value and references its' parent's id value. ID value ranges correspond to generation. It is possible that with more complex genealogical structures the range of id values may need to expand to reduce the probability of two varieties being assigned the same id value.
Usage
nodeToDF(tlist, branch = 0, par.id = NA, id = 1)
Arguments
tlist |
list of varieties |
branch |
of particular variety in the genealogy |
par.id |
the id of the parent |
id |
id offset |
Returns the image object to show the ancestors and descendants of a variety
Description
Returns the image object to show the ancestors and descendants of a variety, with the variety highlighted, if desired
Usage
plotAncDes(v1, geneal, mAnc = 3, mDes = 3, vColor = "#D35C79")
Arguments
v1 |
the label of the vertex of interest (in character string format) |
geneal |
the full genealogy (in data frame format) |
mAnc |
the maximum number of generations of ancestors of v1 to be displayed (in numeric format) |
mDes |
the maximum number of generations of descendants of v1 to be displayed (in numeric format) |
vColor |
the color of the text of the main variety |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
plotAncDes("Tokyo", sbGeneal, vColor = "red")
plotAncDes("Essex", sbGeneal, 2, 3, "blue") + ggplot2::labs(x = "Generation index", y = "")
Returns the image object to show the heat map of degrees between the inputted set of vertices
Description
Returns the image object to show the heat map of degrees between the inputted set of vertices
Usage
plotDegMatrix(varieties, ig, geneal)
Arguments
varieties |
subset of varieties used to generate the heat map |
ig |
the graph representation of the data genealogy (in igraph format) |
geneal |
the full genealogy (in data frame format) |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
See Also
https://www.r-project.org for iGraph information
Examples
data(sbGeneal)
ig <- dfToIG(sbGeneal)
varieties <- c("Bedford", "Calland", "Narow", "Pella", "Tokyo", "Young", "Zane")
p <- plotDegMatrix(varieties, ig, sbGeneal)
p + ggplot2::scale_fill_continuous(low = "white", high = "darkgreen")
Construct the graphic object of the path
Description
This function takes the path as input and outputs an ggplot2 object. The image will correctly position the node labels with x-axis representing the node date, and y-axis representing the node path index. Edges between two nodes represent parent-child relationships between those nodes. For visual appeal, there is a grey box that outlines the node label, as well as an underline and overline for each label.
Usage
plotPath(path, geneal, colName, colNameY = "", fontFace = 1)
Arguments
path |
object created from function getPath |
geneal |
the full genealogy (in data frame format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
colNameY |
the name of the second optional column of the data frame that contains the second optional quantitative variable of interest (in character string format). This optional quantitative variable will be plotted on the vertical axis. |
fontFace |
fontface for the two nodes of interest (1=plain, 2=bold, 3=italic, 4=bold-italic), DEFAULT is 1 |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
See Also
getPath for information on input path building
Examples
data(sbGeneal)
ig <- dfToIG(sbGeneal)
pathTN <- getPath("Tokyo", "Narow", sbIG, sbGeneal, "devYear")
plotPath(pathTN, sbGeneal, "devYear")
sbFilt <- sbGeneal[complete.cases(sbGeneal[1:3]),]
sbFiltIG <- dfToIG(sbFilt)
pathCL <- getPath("Clark", "Lawrence", sbFiltIG, sbFilt, "yield")
plotPath(pathCL, sbFilt, "devYear", "yield") + ggplot2::xlab("Dev Year") + ggplot2::ylab("Yield")
Plot a path between two vertices over the full genealogy
Description
This function requires a path and the ig object, and plots the full genealogy with the path highlighted. The image will correctly position the node labels with x-axis representing the node date, and y-axis representing the node path index. Light grey edges between two nodes represent parent-child relationships between those nodes. To enhance the visual understanding of how the path-of-interest fits into the entire graph structure, the nodes within the path are labelled in boldface, and connected with light-green boldfaced edges.
Usage
plotPathOnAll(
path,
geneal,
ig,
colName,
colNameY = "",
bin = 12,
edgeCol = "gray84",
pathEdgeCol = "seagreen",
nodeSize = 3,
pathNodeSize = 3,
pathNodeFont = "bold",
nodeCol = "black",
animate = FALSE
)
Arguments
path |
path as returned from getPath() or a vector of two variety names which exist in ig |
geneal |
the full genealogy (in data frame format) |
ig |
the graph representation of the data genealogy (in igraph format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
colNameY |
the name of the second optional column of the data frame that contains the second optional quantitative variable of interest (in character string format). This optional quantitative variable will be plotted on the vertical axis. |
bin |
the number of bins to determine the vertical positions of nodes (default is 12). For more information on choosing bin size, please visit the ggenealogy vignette |
edgeCol |
color of the non-path edges, default is "gray84" |
pathEdgeCol |
color of the path edges, default is "seagreen" |
nodeSize |
text size of the non-path node labels, default is 3 |
pathNodeSize |
text size of the path node labels, default is 3 |
pathNodeFont |
font face of text of the path node labels ("plain", "italic", "bold", "bold.italic"), default is "bold" |
nodeCol |
color of the non-path node labels, default is black |
animate |
if the plot will have interactive capabilities, default is FALSE |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
See Also
https://www.r-project.org for iGraph information
getPath for information on input path building
Examples
data(sbGeneal)
sb <- sbGeneal[complete.cases(sbGeneal[1:3]),]
ig <- dfToIG(sb)
pathCL <- getPath("Clark", "Lawrence", ig, sb, "yield")
plotPathOnAll(pathCL, sb, ig, "yield", bin = 3, pathEdgeCol = "red") + ggplot2::xlab("Yield")
plotPathOnAll(pathCL, sb, ig, "yield", "devYear") + ggplot2::xlab("Yield") + ggplot2::ylab("Year")
Returns the image object to show the heat map of dates between the inputted set of vertices
Description
Returns the image object to show the heat map of dates between the inputted set of vertices
Usage
plotVariableMatrix(
varieties,
geneal,
colName,
xLab = "Variety",
yLab = "Variety",
legendLab = "Difference in variable"
)
Arguments
varieties |
subset of varieties used to generate the heat map |
geneal |
the full genealogy (in data frame format) |
colName |
the name of the column of the data frame that contains the quantitative variable of interest (in character string format) |
xLab |
string label on the x axis (default is "Variety") |
yLab |
string label on the y axis (default is "Variety") |
legendLab |
string label on the legend (default is "Degree") |
References
Rutter L, VanderPlas S, Cook D, Graham MA (2019). ggenealogy: An R Package for Visualizing Genealogical Data. Journal of Statistical Software, 89(13), 1–31. doi:10.18637/jss.v089.i13
Examples
data(sbGeneal)
varieties <- c("Bedford", "Calland", "Narow", "Pella", "Tokyo", "Young", "Zane")
p <- plotVariableMatrix(varieties, sbGeneal, "devYear", "Variety", "Variety", "Difference")
p + ggplot2::scale_fill_continuous(low = "white", high = "darkgreen")
Soybean data
Description
This data set contains soy bean genealogical information maintained by the United States Department of Agriculture to be used by plant breeders, geneticists, bioinformaticians, pathologists,and many other research workers.
Usage
data(sbGeneal)
Format
a RData instance, 1 row per each child-parent relationship between soybean varieties
A data frame with 412 rows and 7 variables
Details
Soybean genealogical data
This data contains information on copy number variants, single nucleotide polymorphisms, protein content, and yield, of soybeans. The available data consists of a data frame structure that contains 412 direct child-parent relationships between pairs of soybean varieties. These data were collected from field trials, genetic studies, and United States Department of Agriculture (USDA) bulletins, and date as early as the first decade of the 1900s.
child name of child soybean variety
devYear year child variety was introduced
yield protein yield
yearImputed whether or not the introduced year of the child variety was imputed
parent name of parent soybean variety
References
"Pedigrees of soybean cultivars released in the United States and Canada." Theodore Hyivitz, C.A. Newell, S.G. Carmer. College of Agriculture, University of Illinois at Urbana-Champaign (1977).
Academic statistics data
Description
This data set contains academic genealogical information from the Mathematics Genealogy Project, a web-based database serviced by the North Dakota State University Department of Mathematics and the American Mathematical Society. Specifically, this data set represents a subset of the Mathematical Genealogy Project that contains all the parent-child relationships where both parent and child received an advanced degree of statistics as of June 6, 2015.
Usage
data(statGeneal)
Format
a RData instance, 1 row per each individual in the Mathematics Genealogy Project with an advanced degree in statistics. If the child had a parent who was also listed as having received an advanced degree in statistics in the Mathematics Genealogy project, then the row also contains the parental information.
A data frame with 8165 rows and 6 variables
Details
Academic statistics genealogical data
This data contains information on copy number variants, single nucleotide polymorphisms, protein content, and yield, of soybeans. The available data consists of a data frame structure that contains 412 direct child-parent relationships between pairs of soybean varieties. These data were collected from field trials, genetic studies, and United States Department of Agriculture (USDA) bulletins, and date as early as the first decade of the 1900s.
child name of the individual who received an advanced degree in statistics
parent name of the individual who mentored the child and also received an advanced degree in statistics. If the child has no such parent, then this field is an empty string
gradYear year the child received their advanced degree in statistics
country country from which the child received their advanced degree in statistics
school school from which the child received their advanced degree in statistics
thesis title of the thesis the child submitted to receive their advanced degree in statistics. If this information is not available, then this field is an empty string
References
North Dakota State University and American Mathematical Society (2010). The Mathematics Genealogy Project. Archived Web Site. Retrieved from the Library of Congress, Accessed on March 6, 2015, URL http://www.genealogy.math.ndsu.nodak.edu.