Merge pull request #60 from federicomarini/mosdefied-genetonic

Mosdefied genetonic
federicomarini · Sep 22, 2024 · 67e5c4a · 67e5c4a
2 parents b8a7f7f + 9668bf4
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: GeneTonic
 Title: Enjoy Analyzing And Integrating The Results From Differential Expression 
     Analysis And Functional Enrichment Analysis
-Version: 2.9.0
-Date: 2024-03-24
+Version: 2.99.0
+Date: 2024-09-22
 Authors@R: 
     c(
         person(
@@ -51,6 +51,7 @@ Imports:
     igraph,
     matrixStats,
     methods,
+    mosdef (>= 1.1.0),
     plotly,
     RColorBrewer,
     rintrojs,
@@ -84,7 +85,7 @@ Encoding: UTF-8
 VignetteBuilder: knitr
 URL: https://github.com/federicomarini/GeneTonic
 BugReports: https://github.com/federicomarini/GeneTonic/issues
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 biocViews:
     GUI, GeneExpression, Software, Transcription, Transcriptomics, Visualization,

diff --git a/NAMESPACE b/NAMESPACE
@@ -152,6 +152,15 @@ importFrom(igraph,strength)
 importFrom(igraph,vcount)
 importFrom(matrixStats,rowSds)
 importFrom(methods,is)
+importFrom(mosdef,create_link_GO)
+importFrom(mosdef,create_link_GeneCards)
+importFrom(mosdef,create_link_NCBI)
+importFrom(mosdef,deresult_to_df)
+importFrom(mosdef,gene_plot)
+importFrom(mosdef,geneinfo_to_html)
+importFrom(mosdef,go_to_html)
+importFrom(mosdef,map_to_color)
+importFrom(mosdef,styleColorBar_divergent)
 importFrom(plotly,add_trace)
 importFrom(plotly,ggplotly)
 importFrom(plotly,layout)
@@ -187,6 +196,7 @@ importFrom(utils,browseURL)
 importFrom(utils,citation)
 importFrom(utils,data)
 importFrom(utils,head)
+importFrom(utils,packageDescription)
 importFrom(utils,read.delim)
 importFrom(utils,sessionInfo)
 importFrom(utils,write.table)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+# GeneTonic 2.99.0
+
+## Other notes
+
+* The transition to the functions available in the `mosdef` Bioconductor is complete, with the original functions now being deprecated. This applies to `goseqTable()` (now replaced by `mosdef::run_goseq()`), which has now been made faster and more robust in its functionality and in the ways it can be executed
+* The gene plot widgets now also use the `gene_plot()` function from `mosdef`, instead of the previous `ggplotCounts()` function - `gene_plot()` is more flexible and has more options to control the behavior of the final plot object
+* The `deseqresult2tbl()` and `deseqresult2DEgenes()` are now replaced by the more flexible `mosdef::deresult_to_df()`
+* The internally defined `createLinkENS()`, `createLinkGeneSymbol()`, and `createLinkGO()` are now replaced by the equivalent functions in `mosdef`
+* The Roxygen-based documentation now supports markdown. No visible changes should appear to the user, as the content should have stayed fairly the same
+* Although no visible changes for the end user are expected, the incoming major version bump will reflect the change in the dependency graph, ensuring that this is noticed at least at the version numbering level
+
+
 # GeneTonic 2.8.0
 
 ## Other notes

diff --git a/R/GeneTonic-extras.R b/R/GeneTonic-extras.R
@@ -27,7 +27,7 @@
 #' with a set of unambiguous identifiers (e.g. ENSEMBL ids) and `gene_name`,
 #' containing e.g. HGNC-based gene symbols. This object can be constructed via
 #' the `org.eg.XX.db` packages, e.g. with convenience functions such as
-#' [pcaExplorer::get_annotation_orgdb()].
+#' [mosdef::get_annotation_orgdb()].
 #'
 #' @return A `GeneTonic`-list object, containing in its named slots the arguments
 #' specified above: `dds`, `res_de`, `res_enrich`, and `annotation_obj` - the names
@@ -193,60 +193,15 @@ describe_gtl <- function(gtl) {
 #' go_2_html("GO:0043368")
 go_2_html <- function(go_id,
                       res_enrich = NULL) {
-  fullinfo <- GOTERM[[go_id]]
-  if (is.null(fullinfo)) {
-    return(HTML("Gene Ontology term not found!"))
-  }
-  # extracting the field/component values
-  go_linkbutton <- .link2amigo(GOID(fullinfo))
-  go_term <- Term(fullinfo)
-  go_ontology <- Ontology(fullinfo)
-  go_definition <- Definition(fullinfo)
-  go_synonims <- paste0(
-    unlist(
-      lapply(Synonym(fullinfo), function(arg) {
-        paste0(tags$b("Synonym: "), arg, tags$br())
-      })
-    ),
-    collapse = ""
-  )
-  go_secondary <- Secondary(fullinfo)
-  if (!is.null(res_enrich)) {
-    go_pvalue <- res_enrich[(res_enrich$gs_id == go_id), "gs_pvalue"]
-    go_zscore <- ifelse(
-      "z_score" %in% colnames(res_enrich),
-      format(round(res_enrich[(res_enrich$gs_id == go_id), "z_score"], 2), nsmall = 2),
-      "NA - not yet computed"
-    )
-    go_aggrscore <- ifelse(
-      "aggr_score" %in% colnames(res_enrich),
-      format(round(res_enrich[(res_enrich$gs_id == go_id), "aggr_score"], 2), nsmall = 2),
-      "NA - not yet computed"
-    )
-  }
-  # assembling them together
-  mycontent <- paste0(
-    tags$b("GO ID: "), go_linkbutton, tags$br(),
-    tags$b("Term: "), go_term, tags$br(),
-    ifelse(
-      !is.null(res_enrich),
-      paste0(tags$b("p-value: "), go_pvalue, tags$br(),
-        tags$b("Z-score: "), go_zscore, tags$br(),
-        tags$b("Aggregated score: "), go_aggrscore, tags$br(),
-        collapse = ""
-      ),
-      ""
-    ),
-    tags$b("Ontology: "), go_ontology, tags$br(), tags$br(),
-    tags$b("Definition: "), go_definition, tags$br(),
-    go_synonims,
-    ifelse(
-      length(go_secondary) > 0,
-      paste0(tags$b("Secondary: "), go_secondary, collapse = ""),
-      ""
-    )
-  )
-  return(HTML(mycontent))
+  .Deprecated(old = "go_2_html", new = "mosdef::go_to_html", 
+              msg = paste0(
+                "Please use `mosdef::go_to_html()` in replacement of the `go_2_html()` function, ",
+                "originally located in the GeneTonic package. \nCheck the manual page for ",
+                "`?mosdef::go_to_html()` to see the details on how to use it"))
+
+  mycontent <- mosdef::go_to_html(go_id = go_id,
+                                  res_enrich = res_enrich)
+  return(mycontent)
 }
 
 #' Link to the AmiGO database
@@ -256,12 +211,13 @@ go_2_html <- function(go_id,
 #' @return HTML for an action button
 #' @noRd
 .link2amigo <- function(val) {
-  sprintf(
-    '<a href = "http://amigo.geneontology.org/amigo/term/%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',
-    val,
-    .actionbutton_biocstyle,
-    val
-  )
+  .Deprecated(old = ".link2amigo", new = "mosdef::create_link_GO", 
+              msg = paste0(
+                "Please use `mosdef::create_link_GO()` in replacement of the `.link2amigo()` function, ",
+                "originally located in the GeneTonic package. \nCheck the manual page for ",
+                "`?mosdef::create_link_GO()` to see the details on how to use it"))
+
+  mosdef::create_link_GO(val = val)
 }
 
 #' Information on a gene
@@ -287,41 +243,16 @@ go_2_html <- function(go_id,
 #' geneinfo_2_html("Pf4")
 geneinfo_2_html <- function(gene_id,
                             res_de = NULL) {
-  gene_ncbi_button <- .link2ncbi(gene_id)
-  gene_genecards_button <- .link2genecards(gene_id)
-  gene_gtex_button <- .link2gtex(gene_id)
-
-  if (!is.null(res_de)) {
-    gid <- match(gene_id, res_de$SYMBOL)
-    if (is.na(gid)) {
-      message(
-        "Could not find the specified gene (`", gene_id,
-        "`) in the `res_de` object. \n",
-        "Still, the general HTML content has been generated."
-      )
-      gene_adjpvalue <- tags$em("not found")
-      gene_logfc <- tags$em("not found")
-    } else {
-      gene_adjpvalue <- format(res_de[gid, "padj"])
-      gene_logfc <- format(round(res_de[gid, "log2FoldChange"], 2), nsmall = 2)
-    }
-  }
-
-  mycontent <- paste0(
-    tags$b(gene_id), tags$br(),
-    "Link to the NCBI Gene database: ", gene_ncbi_button, tags$br(),
-    "Link to the GeneCards database: ", gene_genecards_button, tags$br(),
-    "Link to the GTEx Portal: ", gene_gtex_button, tags$br(),
-    ifelse(
-      !is.null(res_de),
-      paste0(tags$b("DE p-value (adjusted): "), gene_adjpvalue, tags$br(),
-        tags$b("DE log2FoldChange: "), gene_logfc,
-        collapse = ""
-      ),
-      ""
-    )
-  )
-  return(HTML(mycontent))
+  .Deprecated(old = "geneinfo_2_html", new = "mosdef::geneinfo_to_html", 
+              msg = paste0(
+                "Please use `mosdef::geneinfo_to_html()` in replacement of the `geneinfo_2_html()` function, ",
+                "originally located in the GeneTonic package. \nCheck the manual page for ",
+                "`?mosdef::geneinfo_to_html()` to see the details on how to use it"))
+
+  mycontent <- mosdef::geneinfo_to_html(gene_id = gene_id,
+                                        res_de = res_de)
+
+  return(mycontent)
 }
 
 #' Link to NCBI database
@@ -331,12 +262,13 @@ geneinfo_2_html <- function(gene_id,
 #' @return HTML for an action button
 #' @noRd
 .link2ncbi <- function(val) {
-  sprintf(
-    '<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',
-    val,
-    .actionbutton_biocstyle,
-    val
-  )
+  .Deprecated(old = ".link2ncbi", new = "mosdef::create_link_NCBI", 
+              msg = paste0(
+                "Please use `mosdef::create_link_NCBI()` in replacement of the `.link2ncbi()` function, ",
+                "originally located in the GeneTonic package. \nCheck the manual page for ",
+                "`?mosdef::create_link_NCBI()` to see the details on how to use it"))
+
+  mosdef::create_link_NCBI(val = val)
 }
 
 #' Link to the GeneCards database
@@ -346,12 +278,13 @@ geneinfo_2_html <- function(gene_id,
 #' @return HTML for an action button
 #' @noRd
 .link2genecards <- function(val) {
-  sprintf(
-    '<a href = "https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',
-    val,
-    .actionbutton_biocstyle,
-    val
-  )
+  .Deprecated(old = ".link2genecards", new = "mosdef::create_link_GeneCards", 
+              msg = paste0(
+                "Please use `mosdef::create_link_GeneCards()` in replacement of the `.link2genecards()` function, ",
+                "originally located in the GeneTonic package. \nCheck the manual page for ",
+                "`?mosdef::create_link_GeneCards()` to see the details on how to use it"))
+
+  mosdef::create_link_GeneCards(val = val)
 }
 
 #' Link to the GTEx Portal
@@ -361,12 +294,13 @@ geneinfo_2_html <- function(gene_id,
 #' @return HTML for an action button
 #' @noRd
 .link2gtex <- function(val) {
-  sprintf(
-    '<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-dna"></i>%s</a>',
-    val,
-    .actionbutton_biocstyle,
-    val
-  )
+  .Deprecated(old = ".link2gtex", new = "mosdef::create_link_GTEX", 
+              msg = paste0(
+                "Please use `mosdef::create_link_GTEX()` in replacement of the `.link2gtex()` function, ",
+                "originally located in the GeneTonic package. \nCheck the manual page for ",
+                "`?mosdef::create_link_GTEX()` to see the details on how to use it"))
+
+  mosdef::create_link_GTEX(val = val)
 }
 
 
@@ -483,7 +417,7 @@ overlap_jaccard_index <- function(x, y) {
 #' @examples
 #'
 #' data(res_de_macrophage, package = "GeneTonic")
-#' res_df <- deseqresult2df(res_macrophage_IFNg_vs_naive)
+#' res_df <- mosdef::deresult_to_df(res_macrophage_IFNg_vs_naive)
 #' library("magrittr")
 #' library("DT")
 #' DT::datatable(res_df[1:50, ],
@@ -529,13 +463,19 @@ overlap_jaccard_index <- function(x, y) {
 styleColorBar_divergent <- function(data,
                                     color_pos,
                                     color_neg) {
-  max_val <- max(abs(data))
-  JS(
-    sprintf(
-      "isNaN(parseFloat(value)) || value < 0 ? 'linear-gradient(90deg, transparent, transparent ' + (50 + value/%s * 50) + '%%, %s ' + (50 + value/%s * 50) + '%%,%s  50%%,transparent 50%%)': 'linear-gradient(90deg, transparent, transparent 50%%, %s 50%%, %s ' + (50 + value/%s * 50) + '%%, transparent ' + (50 + value/%s * 50) + '%%)'",
-      max_val, color_pos, max_val, color_pos, color_neg, color_neg, max_val, max_val
-    )
+  .Deprecated(old = "styleColorBar_divergent", new = "mosdef::styleColorBar_divergent", 
+              msg = paste0(
+                "Please use `mosdef::styleColorBar_divergent()` in replacement of the `styleColorBar_divergent()` function, ",
+                "originally located in the GeneTonic package. \nCheck the manual page for ",
+                "`?mosdef::styleColorBar_divergent()` to see the details on how to use it"))
+
+  code_ret <- mosdef::styleColorBar_divergent(
+    data = data,
+    color_pos = color_pos,
+    color_neg = color_neg
   )
+
+  return(code_ret)
 }
 
 
@@ -571,22 +511,16 @@ styleColorBar_divergent <- function(data,
 #' )(50)
 #' plot(b, col = map2color(b, pal2), pch = 20, cex = 3)
 map2color <- function(x, pal, symmetric = TRUE, limits = NULL) {
-  if (is.null(limits)) {
-    limits <- range(x)
-  }
+  .Deprecated(old = "map2color", new = "mosdef::map_to_color", 
+              msg = paste0(
+                "Please use `mosdef::map_to_color()` in replacement of the `map2color()` function, ",
+                "originally located in the GeneTonic package. \nCheck the manual page for ",
+                "`?mosdef::map_to_color()` to see the details on how to use it"))
 
-  if (symmetric) {
-    max_val <- max(limits)
-    limits[1] <- -max_val
-    limits[2] <- max_val
-  }
-
-  pal_ret <- pal[findInterval(x, seq(limits[1],
-    limits[2],
-    length.out = length(pal) + 1
-  ),
-  all.inside = TRUE
-  )]
+  pal_ret <- map_to_color(x = x, 
+                          pal = pal,
+                          symmetric = symmetric,
+                          limits = limits)
   return(pal_ret)
 }
 
@@ -641,21 +575,18 @@ check_colors <- function(x) {
 #' @examples
 #' data(res_de_macrophage, package = "GeneTonic")
 #' head(res_macrophage_IFNg_vs_naive)
-#' res_df <- deseqresult2df(res_macrophage_IFNg_vs_naive)
+#' res_df <- mosdef::deresult_to_df(res_macrophage_IFNg_vs_naive)
 #' head(res_df)
 deseqresult2df <- function(res_de, FDR = NULL) {
-  if (!is(res_de, "DESeqResults")) {
-    stop("Not a DESeqResults object.")
-  }
-  res <- as.data.frame(res_de)
-  res <- cbind(rownames(res), res)
-  names(res)[1] <- "id"
-  res$id <- as.character(res$id)
-  res <- res[order(res$padj), ]
-  if (!is.null(FDR)) {
-    res <- res[!(is.na(res$padj)) & res$padj <= FDR, ]
-  }
-  res
+  .Deprecated(old = "deseqresult2df", new = "mosdef::deresult_to_df", 
+              msg = paste0(
+                "Please use `mosdef::deresult_to_df()` in replacement of the `deseqresult2df()` function, ",
+                "originally located in the GeneTonic package. \nCheck the manual page for ",
+                "`?mosdef::deresult_to_df()` to see the details on how to use it"))
+
+  df <- mosdef::deresult_to_df(res_de = res_de,
+                               FDR = FDR)
+  return(df)
 }
 
 #' Export to sif