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refactor: migrate igraph network_p2p

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Martin Chan 2020-12-18 11:06:06 +00:00
Родитель ef7123ee48
Коммит 8574145fc1
3 изменённых файлов: 101 добавлений и 61 удалений
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1
NAMESPACE
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@ -152,7 +152,6 @@ import(Information)
import(dplyr)
import(ggplot2)
import(ggraph)
import(network)
import(reshape2)
import(scales)
import(tidyselect)

118
R/network_p2p.R
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@ -12,25 +12,40 @@
#' @param data Data frame containing a person-to-person query.
#' @param hrvar String containing the label for the HR attribute.
#' @param return Character vector specifying what to return, defaults to "pdf".
#' Other valid inputs are "plot", "network" and "table". "network" returns the `network`
#' object used to generate the network plot. The "pdf" option is highly recommended over the "plot"
#' option as the PDF export format has significantly higher performance. The "plot" option is highly
#' computationally intensive and is not generally recommended.
#' Valid inputs are:
#' - "pdf": saves the network plot as a PDF in the specified path. See `path`. This is the recommended
#' output format as large networks can be slow in other formats.
#' - "plot": returns a ggplot object of the network plot. It is not recommended that you run this without
#' assigning the output to an object as plotting to the R console can be slow for large networks.
#' - "table": returns the edgelist data frame used in the network.
#' - "network": returns the igraph object used to create the network plot.
#' @param path File path for saving the PDF output. Defaults to "network_p2p".
#' @param bg_fill String to specify background fill colour.
#' @param font_col String to specify font and link colour.
#' @param legend_pos String to specify position of legend. Defaults to "bottom". See `ggplot2::theme()`.
#' @param palette Function for generating a colour palette with a single argument `n`. Uses `rainbow()` by default.
#' @param ... Additional arguments to pass to `GGally::ggnet2()`.
#' For instance, you may specify the argument `mode` to change the node placement algorithm.
#' @param palette Function for generating a colour palette with a single argument `n`. Uses "rainbow" by default.
#' @param node_alpha A numeric value between 0 and 1 to specify the transparency of the nodes.
#' @param algorithm String to specify the node placement algorithm to be used. Defaults to "fr" for the force-directed
#' algorithm of Fruchterman and Reingold. See <https://rdrr.io/cran/ggraph/man/layout_tbl_graph_igraph.html> for a
#' full list of options.
#'
#' @details
#' For specifying the node placement algorithm, please see the `gplot.layout` documentation for the **sna**
#' package, which provides a full list of the valid functions that can be passed into the `mode` argument.
#' @examples
#' ## Simulate simple P2P network
#' sim_net <-
#' data.frame(TieOrigin_PersonId = sample(seq(1, 100), size = 100, replace = TRUE),
#' TieDestination_PersonId = sample(seq(1, 100), size = 100, replace = TRUE)) %>%
#' dplyr::mutate(TieOrigin_Organization = ifelse(TieOrigin_PersonId >= 50, "A", "B"),
#' TieDestination_Organization = ifelse(TieDestination_PersonId >= 50, "A", "B"),
#' StrongTieScore = rep(1, 100))
#'
#' ## Run plot
#' ## ONLY return 'plot' instead of 'pdf' when data size is small
#' network_p2p(data = sim_net,
#' hrvar = "Organization",
#' return = "plot")
#'
#' @import ggplot2
#' @import dplyr
#' @import network
#' @importFrom grDevices rainbow
#'
#' @export
@ -42,44 +57,52 @@ network_p2p <- function(data,
font_col = "#FFFFFF",
legend_pos = "bottom",
palette = "rainbow",
...){
data <-
data %>%
filter(StrongTieType > 0)
node_alpha = 0.7,
algorithm = "fr"){
## No filtering
tieorigin_var <- paste0("TieOrigin_", hrvar)
tiedestin_var <- paste0("TieDestination_", hrvar)
## Extract edge list
strong_edgelist <-
## Set edges df
edges <-
data %>%
select(TieOrigin_PersonId, TieDestination_PersonId)
select(from = "TieOrigin_PersonId",
to = "TieDestination_PersonId",
weight = "StrongTieScore") %>%
select(-weight) # Overwrite - no info on edge
## Create basic network object
mynet <-
network::network(strong_edgelist, matrix.type="edgelist")
## Vertices data frame to provide meta-data
vert_ft <-
rbind(
# TieOrigin
edges %>%
left_join(select(data, TieOrigin_PersonId, tieorigin_var),
by = c("from" = "TieOrigin_PersonId")) %>%
select(node = "from", !!sym(hrvar) := tieorigin_var),
## Extract list of nodes from network object
myedges <- data.frame(PersonId = network.vertex.names(mynet))
# TieDestination
edges %>%
left_join(select(data, TieDestination_PersonId, tiedestin_var),
by = c("to" = "TieDestination_PersonId")) %>%
select(node = "to", !!sym(hrvar) := tiedestin_var)
)
## Extract attributes
totalAttributes <-
bind_rows(select(data, PersonId = "TieOrigin_PersonId", !!sym(hrvar) := tieorigin_var),
select(data, PersonId = "TieOrigin_PersonId", !!sym(hrvar) := tiedestin_var)) %>%
unique()
## Merge list of nodes and attributes
myedges <- merge(myedges, totalAttributes, by = "PersonId", all.x = TRUE)
## Add attributes to network object
mynet %v% hrvar <- myedges[[hrvar]]
## Create igraph object
g <-
igraph::graph_from_data_frame(edges,
directed = FALSE, # Directed, but FALSE for visualization
vertices = unique(vert_ft)) %>% # remove duplicates
igraph::simplify()
## Palette
## Create tibble
pal <-
tibble(!!sym(hrvar) := g %>%
igraph::get.vertex.attribute(hrvar) %>%
unique())
pal <- tibble(!!sym(hrvar) := unique(myedges[[hrvar]]))
## Apply palette function
col_pal <- do.call(what = palette, args = list(nrow(pal)))
## named character vector
@ -90,24 +113,21 @@ network_p2p <- function(data,
if(return == "table"){
data
edges
} else if(return == "network"){
mynet
g
} else if(return %in% c("plot", "pdf")){
outputPlot <-
mynet %>%
GGally::ggnet2(size = 1,
color = hrvar,
label = FALSE,
edge.size = .01,
edge.alpha = .15,
node.alpha = .8,
palette = pal,
...) +
g %>%
ggraph::ggraph(layout = "igraph", algorithm = algorithm) +
ggraph::geom_edge_link(colour = "lightgrey", edge_width = 0.01, alpha = 0.15) +
ggraph::geom_node_point(aes(colour = !!sym(hrvar)), alpha = node_alpha) +
scale_colour_discrete(type = pal) +
theme_void() +
theme(legend.position = legend_pos,
legend.background = element_rect(fill = bg_fill),
plot.background = element_rect(fill = bg_fill),

43
man/network_p2p.Rd
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@ -13,7 +13,8 @@ network_p2p(
font_col = "#FFFFFF",
legend_pos = "bottom",
palette = "rainbow",
...
node_alpha = 0.7,
algorithm = "fr"
)
}
\arguments{
@ -22,10 +23,15 @@ network_p2p(
\item{hrvar}{String containing the label for the HR attribute.}
\item{return}{Character vector specifying what to return, defaults to "pdf".
Other valid inputs are "plot", "network" and "table". "network" returns the \code{network}
object used to generate the network plot. The "pdf" option is highly recommended over the "plot"
option as the PDF export format has significantly higher performance. The "plot" option is highly
computationally intensive and is not generally recommended.}
Valid inputs are:
\itemize{
\item "pdf": saves the network plot as a PDF in the specified path. See \code{path}. This is the recommended
output format as large networks can be slow in other formats.
\item "plot": returns a ggplot object of the network plot. It is not recommended that you run this without
assigning the output to an object as plotting to the R console can be slow for large networks.
\item "table": returns the edgelist data frame used in the network.
\item "network": returns the igraph object used to create the network plot.
}}
\item{path}{File path for saving the PDF output. Defaults to "network_p2p".}
@ -35,16 +41,31 @@ computationally intensive and is not generally recommended.}
\item{legend_pos}{String to specify position of legend. Defaults to "bottom". See \code{ggplot2::theme()}.}
\item{palette}{Function for generating a colour palette with a single argument \code{n}. Uses \code{rainbow()} by default.}
\item{palette}{Function for generating a colour palette with a single argument \code{n}. Uses "rainbow" by default.}
\item{...}{Additional arguments to pass to \code{GGally::ggnet2()}.
For instance, you may specify the argument \code{mode} to change the node placement algorithm.}
\item{node_alpha}{A numeric value between 0 and 1 to specify the transparency of the nodes.}
\item{algorithm}{String to specify the node placement algorithm to be used. Defaults to "fr" for the force-directed
algorithm of Fruchterman and Reingold. See \url{https://rdrr.io/cran/ggraph/man/layout_tbl_graph_igraph.html} for a
full list of options.}
}
\description{
Pass a data frame containing a person-to-person query and save a network
plot as a PDF file.
}
\details{
For specifying the node placement algorithm, please see the \code{gplot.layout} documentation for the \strong{sna}
package, which provides a full list of the valid functions that can be passed into the \code{mode} argument.
\examples{
## Simulate simple P2P network
sim_net <-
data.frame(TieOrigin_PersonId = sample(seq(1, 100), size = 100, replace = TRUE),
TieDestination_PersonId = sample(seq(1, 100), size = 100, replace = TRUE)) \%>\%
dplyr::mutate(TieOrigin_Organization = ifelse(TieOrigin_PersonId >= 50, "A", "B"),
TieDestination_Organization = ifelse(TieDestination_PersonId >= 50, "A", "B"),
StrongTieScore = rep(1, 100))
## Run plot
## ONLY return 'plot' instead of 'pdf' when data size is small
network_p2p(data = sim_net,
hrvar = "Organization",
return = "plot")
}