From f8ab990aa7563586f24f0d501cdbd467c55746a2 Mon Sep 17 00:00:00 2001 From: Ege Ulgen Date: Mon, 14 Oct 2024 10:03:34 +0100 Subject: [PATCH] fixes #214 --- R/visualization.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/visualization.R b/R/visualization.R index 7b6a75d7..e23c9bba 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -373,7 +373,7 @@ color_kegg_pathway <- function(pw_id, change_vec, scale_vals = TRUE, node_cols = # create pathway graph object and collect all pathway genes g <- tryCatch({ - ggkegg::pathway(pid = pw_id, directory = tempdir(), use_cache = FALSE) + ggkegg::pathway(pid = pw_id, directory = tempdir()) }, error = function(e) { message(paste("Cannot parse KEGG pathway for:", pw_id)) message("Here's the original error message:") @@ -426,7 +426,7 @@ color_kegg_pathway <- function(pw_id, change_vec, scale_vals = TRUE, node_cols = p <- ggraph::ggraph(g, layout="manual", x=igraph::V(g)$x, y=igraph::V(g)$y) p <- p + ggkegg::geom_node_rect(ggplot2::aes(filter = !is.na(.data$change_value), fill = .data$change_value)) - p <- p + ggkegg::overlay_raw_map(pw_id, directory = tempdir(), use_cache = FALSE) + p <- p + ggkegg::overlay_raw_map(pw_id, directory = tempdir()) p <- p + ggplot2::scale_fill_gradient2(low = low_col, mid = mid_col, high = high_col) p <- p + ggplot2::theme_void() p <- p + ggplot2::theme(