clear the rcmdcheck notes

noriakis · Apr 17, 2024 · 944e160 · 944e160
1 parent d3861a6
commit 944e160
Show file tree

Hide file tree

Showing 10 changed files with 45 additions and 43 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -83,6 +83,7 @@ importFrom(GetoptLong,qqcat)
 importFrom(MASS,cov.trob)
 importFrom(NLP,ngrams)
 importFrom(NLP,words)
+importFrom(RColorBrewer,brewer.pal)
 importFrom(XML,xmlElementsByTagName)
 importFrom(XML,xmlParse)
 importFrom(XML,xmlTreeParse)

diff --git a/R/alliance.R b/R/alliance.R
@@ -1,6 +1,6 @@
-#' alliance
 #' @rdname generalf
 #' @export
+#' @importFrom RColorBrewer brewer.pal
 #' @examples
 #' geneList <- c("DDX41","PNKP","ERCC1","IRF3","XRCC1")
 #' \dontrun{alliance(geneList)}
@@ -132,6 +132,12 @@ alliance <- function (geneList,
     ## If filter by GO terms
     if (filterByGO) {
         qqcat("`filterByGO` option enabled. Filtering by GO terms ...\n")
+        data_env <- new.env(parent = emptyenv())
+        load(system.file("extdata", "sysdata.rda", package = "biotextgraph"),
+            envir=data_env)
+        goWords <- data_env[["goWords"]]
+        goWords2gram <- data_env[["goWords2gram"]]
+
         if (ngram==1) {
             filtered_by_GO <- names(matSorted)[tolower(names(matSorted)) %in% goWords]
             matSorted <- matSorted[filtered_by_GO]

diff --git a/R/bugsigdb.R b/R/bugsigdb.R
@@ -1,7 +1,3 @@
-#' bugsigdb
-#' 
-#' Visualize BugSigDB
-#' 
 #' @rdname generalf
 #' @import tm
 #' @import bugsigdbr

diff --git a/R/exportWCNetwork.R b/R/exportWCNetwork.R
@@ -20,6 +20,7 @@
 #' @param sizeMin minimum scale size for nodes
 #' @param sizeMax maximum scale size for nodes
 #' @param wcScale scaling size for wordcloud
+#' @importFrom RColorBrewer brewer.pal
 #' @return export the Cytoscape.js network
 #' @export
 exportWCNetwork <- function(g, geneList, dir="network", colors=NULL,

diff --git a/R/getWordsOnDendro.R b/R/getWordsOnDendro.R
@@ -356,7 +356,7 @@ getWordsOnDendro <- function(dhc, geneVec, geneNumLimit=1000,
                         filter(.data$yend==h1) %>%
                         filter(.data$xend <= max(labs1_x)) %>%
                         filter(.data$xend >= min(labs1_x)) %>%
-                        dplyr::pull(x) %>% unique()                      
+                        dplyr::pull(.data$x) %>% unique()                      
                   }
 
                   labs2_x <- labelPos %>%
@@ -368,7 +368,7 @@ getWordsOnDendro <- function(dhc, geneVec, geneNumLimit=1000,
                     filter(.data$yend==h2) %>%
                     filter(.data$xend <= max(labs2_x)) %>%
                     filter(.data$xend >= min(labs2_x)) %>%
-                    dplyr::pull(x) %>% unique()
+                    dplyr::pull(.data$x) %>% unique()
                   }
                   XMIN <- median(c(min1, min2))
                 } else {
@@ -399,7 +399,7 @@ getWordsOnDendro <- function(dhc, geneVec, geneNumLimit=1000,
                         filter(.data$yend==h1) %>%
                         filter(.data$xend <= max(labs1_x)) %>%
                         filter(.data$xend >= min(labs1_x)) %>%
-                        dplyr::pull(x) %>% unique()                      
+                        dplyr::pull(.data$x) %>% unique()                      
                   }
 
                   labs2_x <- labelPos %>%
@@ -411,7 +411,7 @@ getWordsOnDendro <- function(dhc, geneVec, geneNumLimit=1000,
                         filter(.data$yend==h2) %>%
                         filter(.data$xend <= max(labs2_x)) %>%
                         filter(.data$xend >= min(labs2_x)) %>%
-                        dplyr::pull(x) %>% unique()
+                        dplyr::pull(.data$x) %>% unique()
                   }
 
                   XMAX <- median(c(max1, max2))

diff --git a/R/manual.R b/R/manual.R
@@ -1,13 +1,8 @@
-#' manual
-#' 
-#' Produce networks using manual input.
-#' 
 #' @rdname generalf
 #' @examples
 #' ret <- refseq("DDX41", plotType="wc")
 #' manual(getSlot(ret, "rawText")$Gene_summary, plotType="wc")
 #' @export
-#' @return list of data frame and ggplot2 object
 #' @import tm
 #' @import GeneSummary
 #' @import wordcloud
@@ -160,6 +155,12 @@ manual <- function(df, madeUpper=NULL,
     ## If filter by GO terms
     if (filterByGO) {
         qqcat("`filterByGO` option enabled. Filtering by GO terms ...\n")
+        data_env <- new.env(parent = emptyenv())
+        load(system.file("extdata", "sysdata.rda", package = "biotextgraph"),
+            envir=data_env)
+        goWords <- data_env[["goWords"]]
+        goWords2gram <- data_env[["goWords2gram"]]
+
         if (ngram==1) {
             filtered_by_GO <- names(matSorted)[tolower(names(matSorted)) %in% goWords]
             matSorted <- matSorted[filtered_by_GO]

diff --git a/R/pubmed.R b/R/pubmed.R
@@ -1,11 +1,6 @@
-#' pubmed
-#' 
-#' make word cloud or correlation network from PubMed
-#' 
 #' @rdname generalf
 #' @export
 #' @examples \dontrun{pubmed("DDX41")}
-#' @return object consisting of data frame and ggplot2 object
 #' @import tm
 #' @import GeneSummary
 #' @import wordcloud
@@ -216,14 +211,20 @@ pubmed <- function(queries, useRawQuery=FALSE,
 
     ## If filter by GO terms
     if (filterByGO) {
-    	qqcat("`filterByGO` option enabled. Filtering by GO terms ...\n")
-    	if (ngram==1) {
-	    	filtered_by_GO <- names(matSorted)[tolower(names(matSorted)) %in% goWords]
-	    	matSorted <- matSorted[filtered_by_GO]
-    	} else if (ngram==2) {
+        qqcat("`filterByGO` option enabled. Filtering by GO terms ...\n")
+        data_env <- new.env(parent = emptyenv())
+        load(system.file("extdata", "sysdata.rda", package = "biotextgraph"),
+            envir=data_env)
+        goWords <- data_env[["goWords"]]
+        goWords2gram <- data_env[["goWords2gram"]]
+
+        if (ngram==1) {
+            filtered_by_GO <- names(matSorted)[tolower(names(matSorted)) %in% goWords]
+            matSorted <- matSorted[filtered_by_GO]
+        } else if (ngram==2) {
             filtered_by_GO <- names(matSorted)[tolower(names(matSorted)) %in% goWords2gram]
-	    	matSorted <- matSorted[filtered_by_GO]    		
-    	} else {# Do nothing
+            matSorted <- matSorted[filtered_by_GO]          
+        } else {# Do nothing
         }
     }
 

diff --git a/R/refseq.R b/R/refseq.R
@@ -2,10 +2,10 @@
 #' 
 #' @description Text mining RefSeq description, PubMed, BugSigDB
 #' and the other manually curated textual data.
-#' @details The main functions of the {{biotextgraph}} package. The functions accepts
+#' @details The main functions of the \pkg{biotextgraph} package. The functions accepts
 #' a character vector of biological entities (such as gene identifiers)
 #' and returns the summarized statistics and visualization
-#' contained in {{biotext}} object.
+#' contained in \code{biotext} object.
 #' 
 #' @param geneList gene ID list
 #' @param queries query ID list
@@ -354,6 +354,12 @@ refseq <- function (geneList, keyType="SYMBOL",
     ## If filter by GO terms
     if (filterByGO) {
         qqcat("`filterByGO` option enabled. Filtering by GO terms ...\n")
+        data_env <- new.env(parent = emptyenv())
+        load(system.file("extdata", "sysdata.rda", package = "biotextgraph"),
+            envir=data_env)
+        goWords <- data_env[["goWords"]]
+        goWords2gram <- data_env[["goWords2gram"]]
+
         if (ngram==1) {
             filtered_by_GO <- names(matSorted)[tolower(names(matSorted)) %in% goWords]
             matSorted <- matSorted[filtered_by_GO]

diff --git a/R/sc.R b/R/sc.R
@@ -366,14 +366,14 @@ plotReducedDimWithTexts <- function(sce, marker.info,
             YMe <- dens_max$y
 
             new_points <- rbind(new_points,
-                                c(map_group[i],
+                                c(colmap[i,"group"],
                                   XMe - r,
                                   YMe - r,
                                   XMe + r,
                                   YMe + r))
           } else {
             new_points <- rbind(new_points,
-                                c(map_group[i],
+                                c(colmap[i,"group"],
                                   ctr["x"] - min(dist2center),
                                   ctr["y"] - min(dist2center),
                                   ctr["x"] + max(dist2center),

diff --git a/man/generalf.Rd b/man/generalf.Rd