PGRdup (version 0.2.2.1)

ViewProbDup: Visualize the probable duplicate sets retrieved in a ProbDup object

Description

ViewProbDup plots summary visualizations of accessions within the probable duplicate sets retrieved in a ProbDup object according to a grouping factor field(column) in the original database(s).

Usage

ViewProbDup(pdup, db1, db2 = NULL, factor.db1, factor.db2 = NULL, max.count = 30, select, order = "type", main = NULL)

Arguments

pdup

An object of class ProbDup.

db1

A data frame of the PGR passport database.

db2

A data frame of the PGR passport database. Required when pdup was created using more than one KWIC Index.

factor.db1

The db1 column to be considered for grouping the accessions. Should be of class character or factor.

factor.db2

The db2 column to be considered for grouping the accessions. Should be of class character or factor. retrieved.

max.count

The maximum count of probable duplicate sets whose information is to be plotted (see Note).

select

A character vector of factor names in factor.db1 and/or factor.db2 to be considered for grouping accessions (see Note).

order

The order of the type of sets retrieved in the plot. The default is "type" (see Details).

main

The title of the plot.

Value

A list containing the following objects:

Summary1

The summary data.frame of number of accessions per factor level.

Summary2

The summary data.frame of number of accessions and sets per each type of sets classified according to factor levels.

SummaryGrob

A grid graphical object (Grob) of the summary visualization plot.

See Also

ProbDup, DisProbDup, DataClean, ggplot, gridExtra-package

Examples

## Not run: 
# 
# # Method "b and c"
# #=================
# 
# # Load PGR passport databases
# GN1 <- GN1000[!grepl("^ICG", GN1000$DonorID), ]
# GN1$DonorID <- NULL
# GN2 <- GN1000[grepl("^ICG", GN1000$DonorID), ]
# GN2 <- GN2[!grepl("S", GN2$DonorID), ]
# GN2$NationalID <- NULL
# 
# GN1$SourceCountry <- toupper(GN1$SourceCountry)
# GN2$SourceCountry <- toupper(GN2$SourceCountry)
# 
# GN1$SourceCountry <- gsub("UNITED STATES OF AMERICA", "USA", GN1$SourceCountry)
# GN2$SourceCountry <- gsub("UNITED STATES OF AMERICA", "USA", GN2$SourceCountry)
# 
# # Specify as a vector the database fields to be used
# GN1fields <- c("NationalID", "CollNo", "OtherID1", "OtherID2")
# GN2fields <- c("DonorID", "CollNo", "OtherID1", "OtherID2")
# 
# # Clean the data
# GN1[GN1fields] <- lapply(GN1[GN1fields], function(x) DataClean(x))
# GN2[GN2fields] <- lapply(GN2[GN2fields], function(x) DataClean(x))
# y1 <- list(c("Gujarat", "Dwarf"), c("Castle", "Cary"), c("Small", "Japan"),
#            c("Big", "Japan"), c("Mani", "Blanco"), c("Uganda", "Erect"),
#            c("Mota", "Company"))
# y2 <- c("Dark", "Light", "Small", "Improved", "Punjab", "SAM")
# y3 <- c("Local", "Bold", "Cary", "Mutant", "Runner", "Giant", "No.",
#         "Bunch", "Peanut")
# GN1[GN1fields] <- lapply(GN1[GN1fields], function(x) MergeKW(x, y1, delim = c("space", "dash")))
# GN1[GN1fields] <- lapply(GN1[GN1fields], function(x) MergePrefix(x, y2, delim = c("space", "dash")))
# GN1[GN1fields] <- lapply(GN1[GN1fields], function(x) MergeSuffix(x, y3, delim = c("space", "dash")))
# GN2[GN2fields] <- lapply(GN2[GN2fields], function(x) MergeKW(x, y1, delim = c("space", "dash")))
# GN2[GN2fields] <- lapply(GN2[GN2fields], function(x) MergePrefix(x, y2, delim = c("space", "dash")))
# GN2[GN2fields] <- lapply(GN2[GN2fields], function(x) MergeSuffix(x, y3, delim = c("space", "dash")))
# 
# # Remove duplicated DonorID records in GN2
# GN2 <- GN2[!duplicated(GN2$DonorID), ]
# 
# # Generate KWIC index
# GN1KWIC <- KWIC(GN1, GN1fields)
# GN2KWIC <- KWIC(GN2, GN2fields)
# 
# # Specify the exceptions as a vector
# exep <- c("A", "B", "BIG", "BOLD", "BUNCH", "C", "COMPANY", "CULTURE",
#           "DARK", "E", "EARLY", "EC", "ERECT", "EXOTIC", "FLESH", "GROUNDNUT",
#           "GUTHUKAI", "IMPROVED", "K", "KUTHUKADAL", "KUTHUKAI", "LARGE",
#           "LIGHT", "LOCAL", "OF", "OVERO", "P", "PEANUT", "PURPLE", "R",
#           "RED", "RUNNER", "S1", "SAM", "SMALL", "SPANISH", "TAN", "TYPE",
#           "U", "VALENCIA", "VIRGINIA", "WHITE")
# 
# # Specify the synsets as a list
# syn <- list(c("CHANDRA", "AH114"), c("TG1", "VIKRAM"))
# 
# GNdupc <- ProbDup(kwic1 = GN1KWIC, kwic2 = GN2KWIC, method = "c",
#                   excep = exep, fuzzy = TRUE, phonetic = TRUE,
#                   encoding = "primary", semantic = TRUE, syn = syn)
# 
# GNdupcView <- ViewProbDup(GNdupc, GN1, GN2, "SourceCountry", "SourceCountry",
#                          max.count = 30, select = c("INDIA", "USA"), order = "type",
#                          main = "Groundnut Probable Duplicates")
# 
# ## End(Not run)