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Merge pull request #105 from microsoft/feature/network-enhancements
Feature: introduce enhancements to network functions
This commit is contained in:
Martin Chan
GitHub
Коммит
87f6d82b19
4
NEWS.md
4
NEWS.md
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@ -5,7 +5,9 @@ New functions:
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Significant changes to existing functions:
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- `create_rank()` is now able to call `create_rank_combine()` to compute
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averages for pairwise combinations. The `mode` and `plot_mode` arguments are also made available to the key metric wrapper functions of `create_rank()`.
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averages for pairwise combinations. The `mode` and `plot_mode` arguments are
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also made available to the key metric wrapper functions of `create_rank()`.
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- `network_g2g()` now has the option to specify algorithm and node colour.
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# wpa 1.4.0
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103
R/network_g2g.R
103
R/network_g2g.R
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@ -7,8 +7,8 @@
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#'
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#' @description
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#' Pass a data frame containing a group-to-group query and return a network
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#' plot. Automatically handles "Collaborators_within_group" and
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#' "Other_collaborators" within query data.
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#' plot. Automatically handles `"Collaborators_within_group"` and
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#' `"Other_collaborators"` within query data.
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#'
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#' @param data Data frame containing a G2G query.
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#' @param time_investor String containing the variable name for the Time
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@ -17,7 +17,23 @@
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#' column.
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#' @param metric String containing the variable name for metric. Defaults to
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#' `Collaboration_hours`.
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#' @param algorithm String to specify the node placement algorithm to be used.
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#' Defaults to `"fr"` for the force-directed algorithm of Fruchterman and
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#' Reingold. See
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#' <https://rdrr.io/cran/ggraph/man/layout_tbl_graph_igraph.html> for a full
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#' list of options.
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#' @param node_colour String to specify the colour to be used for displaying
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#' nodes. Defaults to `"lightblue"`. If `"vary"` is supplied, a different colour
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#' is shown for each node at random.
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#' @param exc_threshold Exclusion threshold to apply.
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#' @param org_count Optional data frame to provide the size of each organization
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#' in the `collaborator` attribute. The data frame should contain only two
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#' columns:
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#' - Name of the `collaborator` attribute excluding any prefixes, e.g.
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#' `"Organization"`. Must be of character or factor type.
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#' - `"n"`. Must be of numeric type.
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#' Defaults to `NULL`, where node sizes will be fixed.
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#'
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#' @param subtitle String to override default plot subtitle.
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#' @param return String specifying what to return. This must be one of the
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#' following strings:
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@ -52,6 +68,19 @@
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#' metric = "Meeting_hours",
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#' exc_threshold = 0.05)
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#'
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#' # Return a network plot with circle layout
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#' # Vary node colours and add org sizes
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#' org_tb <- hrvar_count(
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#' sq_data,
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#' hrvar = "Organization",
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#' return = "table"
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#' )
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#'
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#' g2g_data %>%
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#' network_g2g(algorithm = "circle",
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#' node_colour = "vary",
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#' org_count = org_tb)
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#'
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#' # Return an interaction matrix
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#' # Minimum arguments specified
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#' g2g_data %>%
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@ -63,7 +92,10 @@ network_g2g <- function(data,
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time_investor = NULL,
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collaborator = NULL,
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metric = "Collaboration_hours",
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algorithm = "fr",
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node_colour = "lightblue",
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exc_threshold = 0.1,
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org_count = NULL,
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subtitle = "Collaboration Across Organizations",
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return = "plot"){
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@ -95,6 +127,11 @@ network_g2g <- function(data,
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}
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## Get string of HR variable
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hrvar_string <- gsub(pattern = "Collaborators_",
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replacement = "",
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x = collaborator)
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## Warn if 'Collaborators Within Group' is not present in data
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if(! "Collaborators Within Group" %in% unique(data[[collaborator]])){
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@ -145,20 +182,70 @@ network_g2g <- function(data,
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mutate(metric_prop = metric_prop * 10) %>%
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igraph::graph_from_data_frame(directed = FALSE)
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# Org count vary by size -------------------------------------------
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if(!is.null(org_count)){
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igraph::V(mynet_em)$org_size <-
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tibble(id = igraph::get.vertex.attribute(mynet_em)$name) %>%
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mutate(id = gsub(pattern = "\n", replacement = " ", x = id)) %>%
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left_join(org_count, by = c("id" = hrvar_string)) %>%
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pull(n)
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} else {
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# Imputed size if not specified
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igraph::V(mynet_em)$org_size <-
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tibble(id = igraph::get.vertex.attribute(mynet_em)$name) %>%
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mutate(id = gsub(pattern = "\n", replacement = " ", x = id)) %>%
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mutate(n = 20) %>%
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pull(n)
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}
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## Plot object
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plot_obj <-
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mynet_em %>%
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ggraph::ggraph(layout = algorithm) +
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ggraph::geom_edge_link(aes(edge_width = metric_prop * 1),
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edge_alpha = 0.5,
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edge_colour = "grey")
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if(return == "network"){
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mynet_em # Return igraph object
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} else {
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## Plot object
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mynet_em %>%
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ggraph::ggraph(layout = "fr") +
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ggraph::geom_edge_link(aes(edge_width = metric_prop * 1), edge_alpha = 0.5, edge_colour = "grey") +
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ggraph::geom_node_point(size = 20, colour = "lightblue") +
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# Custom node colours ----------------------------------------------
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if(node_colour == "vary"){
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plot_obj <-
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plot_obj +
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ggraph::geom_node_point(
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aes(color = name,
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size = org_size),
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alpha = 0.9
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)
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} else {
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plot_obj <-
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plot_obj +
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ggraph::geom_node_point(
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aes(size = org_size),
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colour = node_colour,
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alpha = 0.9
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)
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}
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plot_obj +
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ggraph::geom_node_text(aes(label = name), size = 3, repel = FALSE) +
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ggplot2::theme(panel.background = ggplot2::element_rect(fill = 'white'), legend.position = "none") +
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ggplot2::theme(
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panel.background = ggplot2::element_rect(fill = 'white'),
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legend.position = "none") +
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theme_wpa_basic() +
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scale_size(range = c(1, 30)) +
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labs(title = "Group to Group Collaboration",
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subtitle = subtitle,
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x = "",
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@ -58,8 +58,8 @@
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#' @param seed Seed for the random number generator passed to `leiden::leiden()`
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#' to ensure consistency. Only applicable when `display` is set to `"leiden"`.
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#' @param algorithm String to specify the node placement algorithm to be used.
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#' Defaults to `"fr"` for the force-directed algorithm of Fruchterman and
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#' Reingold. See
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#' Defaults to `"mds"` for the deterministic multi-dimensional scaling of
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#' nodes. See
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#' <https://rdrr.io/cran/ggraph/man/layout_tbl_graph_igraph.html> for a full
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#' list of options.
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#' @param size_threshold Numeric value representing the maximum number of edges
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@ -10,7 +10,10 @@ network_g2g(
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time_investor = NULL,
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collaborator = NULL,
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metric = "Collaboration_hours",
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algorithm = "fr",
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node_colour = "lightblue",
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exc_threshold = 0.1,
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org_count = NULL,
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subtitle = "Collaboration Across Organizations",
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return = "plot"
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)
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@ -20,7 +23,10 @@ g2g_network(
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time_investor = NULL,
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collaborator = NULL,
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metric = "Collaboration_hours",
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algorithm = "fr",
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node_colour = "lightblue",
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exc_threshold = 0.1,
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org_count = NULL,
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subtitle = "Collaboration Across Organizations",
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return = "plot"
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)
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@ -37,8 +43,28 @@ column.}
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\item{metric}{String containing the variable name for metric. Defaults to
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\code{Collaboration_hours}.}
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\item{algorithm}{String to specify the node placement algorithm to be used.
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Defaults to \code{"fr"} for the force-directed algorithm of Fruchterman and
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Reingold. See
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\url{https://rdrr.io/cran/ggraph/man/layout_tbl_graph_igraph.html} for a full
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list of options.}
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\item{node_colour}{String to specify the colour to be used for displaying
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nodes. Defaults to \code{"lightblue"}. If \code{"vary"} is supplied, a different colour
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is shown for each node at random.}
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\item{exc_threshold}{Exclusion threshold to apply.}
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\item{org_count}{Optional data frame to provide the size of each organization
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in the \code{collaborator} attribute. The data frame should contain only two
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columns:
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\itemize{
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\item Name of the \code{collaborator} attribute excluding any prefixes, e.g.
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\code{"Organization"}. Must be of character or factor type.
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\item \code{"n"}. Must be of numeric type.
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Defaults to \code{NULL}, where node sizes will be fixed.
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}}
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\item{subtitle}{String to override default plot subtitle.}
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\item{return}{String specifying what to return. This must be one of the
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@ -64,8 +90,8 @@ argument:
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}
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\description{
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Pass a data frame containing a group-to-group query and return a network
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plot. Automatically handles "Collaborators_within_group" and
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"Other_collaborators" within query data.
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plot. Automatically handles \code{"Collaborators_within_group"} and
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\code{"Other_collaborators"} within query data.
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}
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\examples{
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# Return a network plot
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@ -78,6 +104,19 @@ g2g_data \%>\%
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metric = "Meeting_hours",
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exc_threshold = 0.05)
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# Return a network plot with circle layout
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# Vary node colours and add org sizes
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org_tb <- hrvar_count(
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sq_data,
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hrvar = "Organization",
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return = "table"
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)
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g2g_data \%>\%
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network_g2g(algorithm = "circle",
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node_colour = "vary",
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org_count = org_tb)
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# Return an interaction matrix
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# Minimum arguments specified
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g2g_data \%>\%
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@ -30,8 +30,8 @@ network_leiden(
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\item{font_col}{String to specify font and link colour.}
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\item{algorithm}{String to specify the node placement algorithm to be used.
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Defaults to \code{"fr"} for the force-directed algorithm of Fruchterman and
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Reingold. See
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Defaults to \code{"mds"} for the deterministic multi-dimensional scaling of
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nodes. See
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\url{https://rdrr.io/cran/ggraph/man/layout_tbl_graph_igraph.html} for a full
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list of options.}
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@ -31,8 +31,8 @@ network_louvain(
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of the nodes.}
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\item{algorithm}{String to specify the node placement algorithm to be used.
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Defaults to \code{"fr"} for the force-directed algorithm of Fruchterman and
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Reingold. See
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Defaults to \code{"mds"} for the deterministic multi-dimensional scaling of
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nodes. See
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\url{https://rdrr.io/cran/ggraph/man/layout_tbl_graph_igraph.html} for a full
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list of options.}
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@ -83,8 +83,8 @@ to 0.5.}
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to ensure consistency. Only applicable when \code{display} is set to \code{"leiden"}.}
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\item{algorithm}{String to specify the node placement algorithm to be used.
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Defaults to \code{"fr"} for the force-directed algorithm of Fruchterman and
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Reingold. See
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Defaults to \code{"mds"} for the deterministic multi-dimensional scaling of
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nodes. See
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\url{https://rdrr.io/cran/ggraph/man/layout_tbl_graph_igraph.html} for a full
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list of options.}
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