fix some issues when R CMD check

DESCRIPTION

@@ -38,14 +38,14 @@ Imports:
     stats,
     tidyr,
     utils,
-    yulab.utils (>= 0.2.3)
+    yulab.utils (>= 0.2.3),
+    ggplot2
 Suggests:
     AnnotationHub,
     BiocManager,
     DOSE,
     fanyi (>= 0.1.0),
     ggtangle,
-    jsonlite,
     readr,
     org.Hs.eg.db,
     quarto,

NAMESPACE

@@ -149,11 +149,16 @@ importFrom(enrichplot,goplot)
 importFrom(enrichplot,gseaplot)
 importFrom(enrichplot,heatplot)
 importFrom(enrichplot,ridgeplot)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,geom_label)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,scale_color_manual)
+importFrom(ggplot2,theme_void)
 importFrom(gson,gson)
 importFrom(gson,read.gmt)
 importFrom(gson,read.gmt.wp)
-importFrom(jsonlite,fromJSON)
-importFrom(jsonlite,toJSON)
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
 importFrom(methods,is)
@@ -166,6 +171,7 @@ importFrom(rlang,"%||%")
 importFrom(rlang,.data)
 importFrom(rlang,check_installed)
 importFrom(rlang,quos)
+importFrom(rlang,sym)
 importFrom(stats,formula)
 importFrom(stats,setNames)
 importFrom(tidyr,gather)

R/gson.R

@@ -149,7 +149,7 @@ gson_WP <- function(organism) {
 #'
 #' @examples
 #'  data = data.frame(gene_id = "gene1",
-#'                    go_id = c("GO:0035492", "GO:0009764", "GO:0031063", "GO:0033714", "GO:0036349"))
+#'                    go_id = c("GO:0035492", "GO:0009764", "GO:0031040", "GO:0033714", "GO:0036349"))
 #'  gson_GO_local(data, species = "E. coli")
 gson_GO_local <- function(data,
                      ont = c("ALL", "BP", "CC", "MF"),
@@ -424,4 +424,4 @@ kegg_release = function(db){
   y = readLines(url)
   release <- sub("\\w+\\s+", "", y[grep('Release', y)])
   return(release)
-}
+}

R/interpret.R

@@ -269,6 +269,10 @@ run_agent_synthesizer <- function(pathways, detective_report, context, model, ap
 #' @param n_pathways Number of top significant pathways to include in the analysis. Default is 20.
 #' @param model The LLM model to use. Default is "deepseek-chat". Supported models include "deepseek-chat", "glm-4", "qwen-turbo" etc.
 #' @param api_key The API key for the LLM. If NULL, it tries to fetch from `getOption('yulab_translate')` based on the model.
+#' @param task Task type, default is "interpretation". Other options include "cell_type"/"annotation" and "phenotype"/"phenotyping".
+#' @param prior Optional prior knowledge (e.g., a biological hypothesis) to guide the task.
+#' @param add_ppi Boolean, whether to use PPI network integration.
+#' @param gene_fold_change Named vector of logFC for expression context.
 #' @return A character string containing the LLM-generated interpretation.
 #' @author Guangchuang Yu
 #' @export
@@ -847,7 +851,6 @@ Ensure the response is a valid JSON object. Do not include any markdown formatti
     return(base_prompt)
 }
 
-#' @importFrom jsonlite toJSON fromJSON
 call_llm_fanyi <- function(prompt, model, api_key) {
     if (!requireNamespace("fanyi", quietly = TRUE)) {
         stop("Package 'fanyi' is required for interpret(). Please install it.")

R/plot_interpret.R

@@ -3,7 +3,10 @@
 #' @title plot
 #' @param x An `interpretation` object.
 #' @param layout Graph layout, default is "nicely".
-#' @param ... Additional arguments passed to `ggtangle::ggtangle`.
+#' @param ... Additional arguments passed to `ggplot2::ggplot`.
+#' @importFrom ggplot2 ggplot geom_label geom_point aes scale_color_manual
+#' @importFrom ggplot2 theme_void ggtitle
+#' @importFrom rlang sym
 #' @export
 plot.interpretation <- function(x, layout = "nicely", ...) {
 
@@ -26,8 +29,8 @@ plot.interpretation <- function(x, layout = "nicely", ...) {
     # Add edges
     # We try to map interaction type to color if available
     if ("interaction" %in% igraph::edge_attr_names(g)) {
-        p <- p + ggtangle::geom_edge(ggplot2::aes(color = interaction)) +
-             ggplot2::scale_color_manual(values = c(
+        p <- p + ggtangle::geom_edge(aes(color = !!sym("interaction"))) +
+             scale_color_manual(values = c(
                  activation = "green3", 
                  inhibition = "red3", 
                  repression = "red3",
@@ -40,15 +43,15 @@ plot.interpretation <- function(x, layout = "nicely", ...) {
 
     # Add nodes and labels
     p <- p + geom_point(size = 5, color = "lightblue") + 
-         geom_label(ggplot2::aes(label = name)) +
-         ggplot2::theme_void()
+         geom_label(aes(label = !!sym("name"))) +
+         theme_void()
 
     main_title <- "Refined Regulatory Network"
     if (!is.null(x$cluster)) {
         main_title <- paste0(main_title, " (", x$cluster, ")")
     }
 
-    p <- p + ggplot2::ggtitle(main_title)
+    p <- p + ggtitle(main_title)
 
     return(p)
 }