Merge pull request #116 from cbielow/rm_kableExtra

Remove kableExtra package dependency

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: PTXQC
 Type: Package
 Title: Quality Report Generation for MaxQuant and mzTab Results
-Version: 1.0.12
-Date: 2021-11-02
+Version: 1.0.13
+Date: 2022-03-22
 Author: Chris Bielow [aut, cre],
   Juliane Schmachtenberg [ctb],
   Swenja Wagner [ctb],
@@ -25,9 +25,10 @@ Imports:
     grid,
     grDevices,
     gtable,
+    htmlTable,
     jsonlite,
-    kableExtra,
     knitr (>= 1.10),
+    magrittr,
     methods,
     ontologyIndex,
     plyr,

NAMESPACE

@@ -112,8 +112,9 @@ import(ggplot2)
 import(grDevices)
 import(grid)
 import(gtable)
-import(kableExtra)
+import(htmlTable)
 import(knitr)
+import(magrittr)
 import(methods)
 import(plyr)
 import(reshape2, except = c(dcast, melt))

NEWS

@@ -7,6 +7,9 @@ Versions uploaded to CRAN are marked with [CRAN].
 #########   CHANGELOG  ##########
 #################################
 
+[CRAN] v1.00.13 -- 2022/03/22
+  - [FIX] Remove dependency 'kableExtra' and use 'htmlTable' package instead
+
 [CRAN] v1.00.12 -- 2021/11/02
   - [FIX] Documentation and cosmetic fixes (pr #109)
   - [FIX/DOC] improved legends and better links in Html reports (pr #111)

R/MQDataReader.R

@@ -269,11 +269,11 @@ readMQ = function(file, filter = "", type = "pg", col_subset = NA, add_fs_col =
       .self$mq.data[, int_cols[int_cols_nn]] = sapply(int_cols[int_cols_nn], function(x_name)
       {
         x = .self$mq.data[, x_name]
-        if (class(x) == "integer")
+        if (inherits(x, "integer"))
         {
           x = as.numeric(x)
         }
-        if (class(x) != "numeric")
+        if (!inherits(x, "numeric"))
         {
           cat(paste(x[grep(",", x)], collapse = ",", sep=", "))
           cat(paste(unique(x), collapse = ",", sep=", "))

R/MzQC_classes.R

@@ -87,7 +87,7 @@ isValidMzQC = function(x, ...)
   # anchor
   if (missing(x)) return(TRUE)
 
-  if ("list" %in% class(x)) {
+  if (inherits(x, "list")) {
     idx = sapply(x, isValidMzQC)
     if (any(idx == FALSE)) {
       warning(paste0("In list of '", class(x[[1]]), "', the element(s) #[", paste(which(idx == FALSE), collapse = ","), "] is/are invalid."), immediate. = TRUE, call. = FALSE)
@@ -122,7 +122,7 @@ isValidMzQC = function(x, ...)
 #'   
 fromDatatoMzQC = function(mzqc_class, data)
 {
-  if ("list" %in% class(data))
+  if (inherits(data, "list"))
   {
     return(sapply(data, function(x) {
       obj = mzqc_class$new()
@@ -190,6 +190,9 @@ NULL_to_NA = function(var_or_NULL) {
 #' @examples
 #'    dt1 = MzQCDateTime$new("1900-01-01")
 #'    dt2 = MzQCDateTime$new(Sys.time())
+#'    ## test faulty input
+#'    ## errors with 'character string is not in a standard unambiguous format'
+#'    try(MzQCDateTime$new('lala'), silent=TRUE) 
 #'    ## test roundtrip conversion from/to JSON
 #'    dt2$fromData(jsonlite::fromJSON(jsonlite::toJSON(dt1)))
 #     dt1$datetime == dt2$datetime    ## TRUE
@@ -404,7 +407,7 @@ setMethod('asJSON', 'MzQCinputFile', function(x, ...) x$toJSON(...))
 # x2 = jsonlite::toJSON(nif2)
 # xdata = jsonlite::fromJSON(x, simplifyDataFrame = FALSE)
 # xdata
-# class(fromDatatoMzQC(MzQCcvParameter, xdata$fileProperties)) == "list"
+# inherits(fromDatatoMzQC(MzQCcvParameter, xdata$fileProperties), "list")
 # jsonlite::toJSON(xdata, pretty = TRUE, auto_unbox = T)
 # isValidMzQC(l2)
 # nif$fromData(xdata)

R/PTXQC.R

@@ -31,7 +31,6 @@
 #' @import grid
 #' @import grDevices
 #' @import gtable
-#' @import kableExtra
 #' @import knitr
 #' @import methods
 #' @import plyr

R/createReport.R

@@ -65,7 +65,7 @@ createReport = function(txt_folder = NULL, mztab_file = NULL, yaml_obj = list(),
   ###
   ###  prepare the YAML config
   ###
-  if (class(yaml_obj) != "list")
+  if (!inherits(yaml_obj, "list"))
   {
     stop(paste0("Argument 'yaml_obj' is not of type list\n"));
   }
@@ -375,7 +375,7 @@ createReport = function(txt_folder = NULL, mztab_file = NULL, yaml_obj = list(),
     } 
 
     ### warn of special contaminants!
-    if (class(yaml_param$yaml_contaminants) == "list")  ## SC are requested
+    if (inherits(yaml_param$yaml_contaminants, "list"))  ## SC are requested
     {
       if (!is.null(df_pg))
       {

R/fcn_MQ.R

@@ -47,7 +47,7 @@ boxplotCompare = function(data,
   }
 
   ## shorten group names
-  if (class(names)=='data.frame')
+  if (inherits(names, 'data.frame'))
   {
     stopifnot(sort(colnames(names)) == c("long", "short"))
     data$group = names$short[match(data$group, names$long)]
@@ -58,7 +58,7 @@ boxplotCompare = function(data,
     }
   }
   ## make it a factor
-  if (!("factor" %in% class(data$group))) data$group = factor(data$group)
+  if (!inherits(data$group, "factor")) data$group = factor(data$group)
 
   ## actual number of entries in each column (e.g. LFQ often has 0)
   ncol.stat = plyr::ddply(data, "group", function(x)
@@ -71,7 +71,7 @@ boxplotCompare = function(data,
   data$group2 = ncol.stat$newname[match(data$group, ncol.stat$group)]
 
   ## check (ddply makes  ncol.stat$newname a factor with matching levels)
-  #stopifnot(class(data$group2) == "factor")
+  #stopifnot(inherits(data$group2, "factor"))
   #stopifnot(all(as.numeric(data$group) == as.numeric(data$group2))) ## as.numeric() is meaningless on factors with different levels
   data$group = data$group2
   ## remove -inf and NA's

R/fcn_misc.R

@@ -1292,7 +1292,7 @@ getMetricsObjects = function(DEBUG_PTXQC = FALSE)
 
   lst_qcMetrics = sapply(lst_qcMetrics_str, function(m) {
     q = get(m)
-    if (class(q) %in% "refObjectGenerator"){
+    if (inherits(q, "refObjectGenerator")) {
       return(q$new())
     }
     return(NULL)

R/fcn_miscGGplot.R

@@ -65,7 +65,7 @@ printWithFooter = function(gg_obj, bottom_left = NULL, bottom_right = NULL)
 #' 
 scale_x_discrete_reverse = function(values, ...)
 {
-  if ("factor" %in% class(values)) values = droplevels(values)
+  if (inherits(values, "factor")) values = droplevels(values)
   return (scale_x_discrete(limits = rev(levels(values)), ... ))
 }
 
@@ -80,7 +80,7 @@ scale_x_discrete_reverse = function(values, ...)
 #'
 scale_y_discrete_reverse = function(values, ...)
 {
-  if ("factor" %in% class(values)) values = droplevels(values)
+  if (inherits(values, "factor")) values = droplevels(values)
   return (scale_y_discrete(limits = rev(levels(values)), ... ))
 }
 

R/fcn_plots.R

@@ -712,32 +712,28 @@ plotTableRaw = function(data, colours="black", fill=NA, just="centre")
 #' 
 #' 
 #' @param data A data.frame which serves as table
-#' @param header A set of headlines, e.g. c("top line", "bottom line")
-#' @param font_size Html font size
-#' @return table as character string for cat()'ing into html
+#' @param caption A set of headlines, e.g. c("top line", "bottom line")
+#' @return table as html character string for cat()'ing into an html document
+#'
+#' @import htmlTable
+#' @import magrittr
 #'
 #' @export 
 #' 
 #' @examples
 #'   data = data.frame(raw.file = letters[1:4],
 #'                     id.rate = 3:6)
 #'   getHTMLTable(data, 
-#'                header = "some header line", 
-#'                font_size = 11)
+#'                caption = "some header line")
 #' 
-getHTMLTable = function(data, header = NA, font_size = 12)
+getHTMLTable = function(data, caption = NA)
 {
-  tbl = kableExtra::kable_styling(kableExtra::kable(data, row.names = FALSE, format = "html"),
-                                  bootstrap_options = c("striped", "hover", "condensed"), 
-                                  full_width = FALSE, 
-                                  font_size = font_size)
-
-  if (!any(is.na(header)))
-  {
-    header__ = header;
-    tbl = kableExtra::add_header_above(tbl, c(header__ = ncol(data)))
-    tbl = gsub("header__", paste(header__, sep = "", collapse = "<br>"), as.character(tbl))
-  } 
+
+  tbl = data %>% 
+          addHtmlTableStyle(align = 'l',  ## align columns left
+                            col.rgroup = c("none", "#F7F7F7")) %>%
+          htmlTable(rnames = FALSE,    ## no row names
+                    caption = caption) 
 
   return(tbl)
 }

R/fcn_qualities.R

@@ -258,7 +258,7 @@ qualHighest = function(x, N)
 #'
 qualBestKS = function(x) {
 
-  if (class(x) != "list") stop("Function bestKS() expects a list!")
+  if (!inherits(x, "list")) stop("Function bestKS() expects a list!")
   if (length(x) == 0) stop("Error: qualBestKS() received empty data!")
 
   if (is.null(names(x))) names(x) = 1:length(x)

R/mzQC.R

@@ -3,7 +3,7 @@
 #' Get the information of each CV term from an obo file.
 #' 
 #' @param cv_obo_file A path to an .obo file
-#' @return A list containing cv term information
+#' @return A list containing CV term information
 #' 
 #' 
 parseOBO = function(cv_obo_file){
@@ -190,7 +190,7 @@ assembleMZQC = function(lst_qcMetrics, raw_file_mapping)
   {
     mzqc_data = metric$mzQC
     if (is.null(mzqc_data)) next
-    if (class(mzqc_data) != "list") stop("mzQC member of metric must be of class 'list()'")
+    if (!inherits(mzqc_data, "list")) stop("mzQC member of metric must be of class 'list()'")
     if (length(mzqc_data) == 0) next
     if (any(is.null(names(mzqc_data)))) stop("mzQC member of metric '", metric$qcName, "' is a list, but has no names (must be fc.raw.file names or a concatenation of those)")
 

R/qcMetric.R

@@ -119,7 +119,7 @@ qcMetric = setRefClass("qcMetric",
          }
 
          if (!("plots" %in% names(r))) stop(c("Worker of '", .self$qcName, "' did not return valid result format!"))
-         if (!class(r[["plots"]]) == "list") stop(c("Worker of '", .self$qcName, "' did not return plots in list format!"))
+         if (!inherits(r[["plots"]], "list")) stop(c("Worker of '", .self$qcName, "' did not return plots in list format!"))
 
 
          lpl = flattenList(r[["plots"]])
@@ -141,7 +141,7 @@ qcMetric = setRefClass("qcMetric",
          if (!withTitle) { ## no title
            r = lapply(.self$plots, function(p) {
              ## delete title 
-             if ("ggplot" %in% class(p)) p = p + ggtitle(NULL)
+             if (inherits(p, "ggplot")) p = p + ggtitle(NULL)
              return (p)
            })
            return(r)

R/qcMetric_EVD.R

@@ -864,7 +864,7 @@ qcMetric_EVD_Charge =  setRefClass(
       "Charge distribution per Raw file. For typtic digests, peptides of charge 2 
 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant.
 Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can 
-cause a shift (see [Bittremieux 2017, DOI: 10.1002/mas.21544](https://onlinelibrary.wiley.com/doi/abs/10.1002/mas.21544) ).
+cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544).
 The charge distribution should be similar across Raw files.
 Consistent charge distribution is paramount for comparable 3D-peak intensities across samples.
 

R/qcMetric_PAR.R

@@ -49,7 +49,7 @@ track database completeness and database version information (if given in the fi
 
       ## HTML: alternative table
       ## (do this before line breaks, since Html can handle larger strings)      
-      tbl_f = getHTMLTable(d_par2, header = fasta_files, font_size = 12)
+      tbl_f = getHTMLTable(d_par2, caption = fasta_files)
 
       ## break long values into multiple lines (to preserve PDF table width)
       splitMaxLen = function(s) {

README.md

@@ -9,6 +9,8 @@ PTXQC
 
 ### Latest changes / ChangeLog
 
+
+  - v1.00.13 - Mar 2022: internal changes (removed a deprecated dependency)
   - v1.00.12 - Nov 2021: Documentation and cosmetic fixes (https://github.com/cbielow/PTXQC/pull/109); improved legends, better links in Html reports (https://github.com/cbielow/PTXQC/pull/111); avoid crash on datasets with only a single MS/MS spectrum (https://github.com/cbielow/PTXQC/pull/112)
   - v1.00.11 - Sep 2021: initial support for mzQC Quality Control output (https://github.com/cbielow/PTXQC/pull/105); Missed cleavages can be computed from evidence.txt (https://github.com/cbielow/PTXQC/pull/104); minor fixes
   - v1.00.10 - May 2021: detect non UK/US locale (https://github.com/cbielow/PTXQC/pull/99); Revive missing MBR metrics (https://github.com/cbielow/PTXQC/issues/97); restore full Parameter list (showing MaxQuant parameters (https://github.com/cbielow/PTXQC/issues/101); decoy distribution in MS/MS mass error plot restored (https://github.com/cbielow/PTXQC/issues/102)

inst/examples/report_v1.0.10__txt_5files_withMatch-100min.html

@@ -1159,7 +1159,7 @@ <h3><span class="header-section-number">1.4.9</span> EVD: charge distribution</b
 ↓ Show Help
 </div>
 <div class="helpText">
-<p>Charge distribution per Raw file. For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/mas.21544">Bittremieux 2017, DOI: 10.1002/mas.21544</a> ). The charge distribution should be similar across Raw files. Consistent charge distribution is paramount for comparable 3D-peak intensities across samples.</p>
+<p>Charge distribution per Raw file. For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544). The charge distribution should be similar across Raw files. Consistent charge distribution is paramount for comparable 3D-peak intensities across samples.</p>
 <p>Heatmap score [EVD: Charge]: Deviation of the charge 2 proportion from a representative Raw file (‘qualMedianDist’ function).</p>
 </div>
 </div>