diff options
Diffstat (limited to 'R/networkplot.R')
| -rw-r--r-- | R/networkplot.R | 27 |
1 files changed, 18 insertions, 9 deletions
diff --git a/R/networkplot.R b/R/networkplot.R index 2401cb1..cbea488 100644 --- a/R/networkplot.R +++ b/R/networkplot.R @@ -9,6 +9,8 @@ #' @param R A square numeric matrix with names columns and rows #' @param title Optional plot title #' @param groups Optional data.frame mapping nodes to groups +#' @param group_label Optional string labeling the kind of grouping +#' @param r_label The string naming the relationship type (default 'Correlation') #' #' @return A ggraph object #' @@ -27,7 +29,7 @@ #' @import igraph #' #' @export -networkplot <- function(R, groups = NULL, title = NULL){ +networkplot <- function(R, groups = NULL, group_label = NULL, title = NULL, r_label = 'Correlation'){ Rm <- tryCatch({ if(is.matrix(R)){ if(nrow(R) != ncol(R)) stop('R must be square') @@ -71,6 +73,9 @@ networkplot <- function(R, groups = NULL, title = NULL){ to = colnames(Rm)[idx[,2]], r = Rm[idx] ) + # remove edges where r is zero + edges <- edges[edges$r != 0,] + edges <- edges[order(abs(edges$r)),] # groups must be a data.frame with 2 columns 'node' and 'group' if(!is.null(groups)){ @@ -133,7 +138,7 @@ networkplot <- function(R, groups = NULL, title = NULL){ ggraph::geom_conn_bundle( data = con, ggplot2::aes( - edge_alpha = abs(.data$value)^2, + edge_alpha = abs(.data$value), edge_colour = .data$value ), tension = 0.5 @@ -144,7 +149,8 @@ networkplot <- function(R, groups = NULL, title = NULL){ high = 'blue', midpoint = 0, limits = c(-1, 1), - guide = 'none' + name = r_label, + guide = ggplot2::guide_colourbar() ) + # operates on node data from the layout # leaf is a logical vector (provided by the ggraph object g) @@ -153,16 +159,19 @@ networkplot <- function(R, groups = NULL, title = NULL){ ggraph::geom_node_point( ggplot2::aes( filter = .data$leaf, - fill = .data$group + colour = .data$group ), - size = 1 + size = 2 ) + # labels nodes and groups ggraph::geom_node_text( - ggplot2::aes(label = .data$name), + ggplot2::aes( + filter = .data$leaf, + label = .data$name + ), # prevents text labels from overlapping - repel = TRUE, - size = 1 + hjust = 'outward', + size = 2 ) + ggplot2::theme_void() @@ -176,7 +185,7 @@ networkplot <- function(R, groups = NULL, title = NULL){ if(!is.null(groups)){ p <- p + - ggplot2::scale_fill_discrete(name = 'Superpathway') + ggplot2::scale_colour_discrete(name = group_label) } return(p) |