Fix legends

NEWS

@@ -9,7 +9,7 @@ Versions uploaded to CRAN are marked with [CRAN].
 
 [?] v1.00.12 -- develop
   - [FIX] Documentation and cosmetic fixes (pr #109)
-
+  - [FIX/DOC] improved legends and better links in Html reports (pr #111)
 
 [CRAN] v1.00.11 -- 2021/09/28
   - [FEATURE] initial support for mzQC Quality Control output (pr #105)

R/createReport.R

@@ -684,7 +684,7 @@ createReport = function(txt_folder = NULL, mztab_file = NULL, yaml_obj = list(),
       }
       cat(paste0("HTML TEMPLATE: ", html_template, "\n"))
       out_dir = dirname(rprt_fns$report_file_HTML)
-      file.copy(html_template, out_dir, overwrite = TRUE)
+      file.copy(html_template, out_dir, overwrite = FALSE)
       out_template = file.path(out_dir, basename(html_template))
       ## Rmarkdown: convert to Markdown, and then to HTML (or PDF) ...
       ## Intermediates_dir is required if inputdir!=outputdir, since Shiny server might not allow write-access to input file directory
@@ -721,6 +721,7 @@ createReport = function(txt_folder = NULL, mztab_file = NULL, yaml_obj = list(),
         print(gg_obj)
       }
     }
+    cat("\nCreating PDF ...\n")
     grDevices::pdf(report_file_PDF)
     printWithPage(hm[["plot"]], "p. 1")      # summary heatmap
     printWithPage(pl_nameMapping$plots, "p. 2")    # short file mapping

R/fcn_plots.R

@@ -875,9 +875,12 @@ plot_UncalibratedMSErr = function(data, MQBug_raw_files, stats, y_lim, extra_lim
   ## use augmented name
   data$fc.raw.file_ext = stats$fcr_new_lvl[ match(data$fc.raw.file, stats$fc.raw.file) ]
 
+  cols_sub = c("default"="black", "MQ bug"="red", "out-of-search-tol"="orange")
+  cols_sub = cols_sub[names(cols_sub) %in% data$col]
+
   p = ggplot(data, col=data$col) +
         geom_boxplot(aes_string(x = "fc.raw.file_ext", y = "uncalibrated.mass.error..ppm.", col="col"), varwidth = TRUE, outlier.shape = NA) +
-        scale_colour_manual("", values = c("default"="black", "MQ bug"="red", "out-of-search-tol"="orange"), guide = showColLegend) +
+        scale_colour_manual("", values = cols_sub, guide = showColLegend) +
         ylab(expression(Delta~"mass [ppm]")) +
         xlab("") +
         ylim(y_lim) +
@@ -935,10 +938,13 @@ plot_CalibratedMSErr = function(data, MQBug_raw_files, stats, y_lim, extra_limit
   ## only show legend if special things happen  
   showColLegend = ifelse(length(setdiff(data$col, "default")) > 0, "legend", "none")
 
+  cols_sub = c("default"="black", "MQ bug"="red", "out-of-search-tol"="orange")
+  cols_sub = cols_sub[names(cols_sub) %in% data$col]
+
   ## plot
   p = ggplot(data, col = data$col) +
     geom_boxplot(aes_string(x = "fc.raw.file", y = "mass.error..ppm.", col="col"), varwidth = TRUE, outlier.shape = NA) +
-    scale_colour_manual("", values = c("default"="black", "MQ bug"="red", "out-of-search-tol"="orange"), guide = showColLegend) +
+    scale_colour_manual("", values = cols_sub, guide = showColLegend) +
     ylab(expression(Delta~"mass [ppm]")) +
     xlab("") +
     ylim(y_lim) +

R/qcMetric_EVD.R

@@ -598,11 +598,13 @@ during MaxQuant configuration.
 The resulting residual RT delta after RT alignment (compared to a reference Raw file), is shown as green/red dots. One dot represents
 one peptide (incl. charge). Every dot (peptide) outside an allowed residual delta RT (1min by default) is colored red.
 All others are green.
+The ratio of 'green' vs. 'green+red' peptides is annotated using 'sc: ' (for 'score') in the plot subtitles. High values are better (green peptides dominate).
 
 If moving 'red' dots to the horizontal zero-line (to make them green) requires large RT shifts, then increasing the alignment
 search window might help MaxQuant to find a better alignment.
 
-Heatmap score [EVD: MBR Align]: fraction of 'green' vs. 'green+red' peptides.
+
+Heatmap score [EVD: MBR Align]: ratio of 'green' vs. 'green+red' peptides 
 ",
     workerFcn = function(.self, df_evd, tolerance_matching, raw_file_mapping)
     {

README.md

@@ -9,6 +9,7 @@ PTXQC
 
 ### Latest changes / ChangeLog
 
+  - v???     - 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)
   - 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)
   - v1.00.09 - Jan 2021: output logging to external file (https://github.com/cbielow/PTXQC/issues/94); mzQC support (partial); less warnings;

inst/reportTemplate/PTXQC_report_template.Rmd

@@ -155,19 +155,20 @@ document.getElementById("locale_shorttext").innerHTML = shorttext;
   - navigate using the 'Table of Content' above or just scroll down
   - collapse sections by just clicking their name
   - click on the "↓ Show Help" symbol to see a description for each metric and its scoring
-  - edit the config `r paste0("file:///", gsub("\\\\", "/", rprt_fns$yaml_file))` to
+  - edit the YAML config <a href="`r paste0("file:./", basename(rprt_fns$yaml_file))`">`r paste0("file:./", basename(rprt_fns$yaml_file))`</a> to
      - set the report format (HTML, plainPDF, or both)
      - disable metrics
      - customize the order of metrics
      - set individual target thresholds
-  - edit `r paste0("file:///", gsub("\\\\", "/", rprt_fns$filename_sorting))` to customize
+  - edit `r paste0("file:./", basename(rprt_fns$filename_sorting))` to customize
      - the order of Raw files in plots and heatmap
      - abbreviations of Raw file names
-  - edit the Html template `r paste0("file:///", gsub("\\\\", "/", html_template))` to
+  - edit the Html template `r paste0("file:./", basename(html_template))` to
      - alter the look and feel of this report (e.g. colors, font and image sizes, help texts, etc.)
   - report bugs and file requests via the [GitHub issue tracker](https://github.com/cbielow/PTXQC/issues)
   - full PTXQC manual available [here](https://github.com/cbielow/PTXQC)
 
+
 ## HeatMap
 ```{r MQparams, echo=FALSE, results="asis"}
 hm[["plot"]]