From af4dc4b4af144297bb42c878f06b0703ca4a0b28 Mon Sep 17 00:00:00 2001
From: Johannes Rainer <johannes.rainer@gmail.com>
Date: Thu, 21 Nov 2024 10:32:29 +0100
Subject: [PATCH] Fix mixes 9-11

---
 R/match-standards-chunks.R      |  4 +--
 match-standards-serum-mix09.Rmd | 44 +++++++++++++++++++--------------
 match-standards-serum-mix10.Rmd | 37 ++++++++++++++-------------
 match-standards-serum-mix11.Rmd | 35 +++++++++++++++-----------
 4 files changed, 67 insertions(+), 53 deletions(-)

diff --git a/R/match-standards-chunks.R b/R/match-standards-chunks.R
index 3760c27..9af863f 100644
--- a/R/match-standards-chunks.R
+++ b/R/match-standards-chunks.R
@@ -282,7 +282,7 @@ fts$ion_relative_intensity <- feature_table[fts$feature_id, "mean_high"]
 fts$ion_relative_intensity <- fts$ion_relative_intensity /
     max(fts$ion_relative_intensity)
 fts$ion_adduct <- feature_table[fts$feature_id, "adduct"]
-fts$compound_id <- hmdb_id
+fts$compound_id <- std_dilution$HMDB[std_dilution$name == std]
 fts$polarity <- POLARITY
 idb <- insertIon(idb, fts, addColumns = TRUE)
 pandoc.table(fts, split.tables = Inf, style = "rmarkdown")
@@ -290,7 +290,7 @@ rm(fts)
 
 ## ---- add-ms2-spectra ----
 ms2$original_spectrum_id <- spectraNames(ms2)
-ms2$compound_id <- hmdb_id
+ms2$compound_id <- std_dilution$HMDB[std_dilution$name == std]
 ms2$original_file <- basename(ms2$dataOrigin)
 ms2$collisionEnergy <- 20
 ms2$collisionEnergy[grep("CE30", ms2$original_file)] <- 30
diff --git a/match-standards-serum-mix09.Rmd b/match-standards-serum-mix09.Rmd
index c74a63d..9ffb362 100644
--- a/match-standards-serum-mix09.Rmd
+++ b/match-standards-serum-mix09.Rmd
@@ -297,7 +297,7 @@ ms2$confidence <- c("low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -372,7 +372,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -457,7 +457,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -580,7 +580,7 @@ ms2$confidence <- c("high", "high", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -719,7 +719,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -807,7 +807,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -886,7 +886,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1009,7 +1009,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1094,7 +1094,7 @@ ms2$confidence <- c("low", "low", "high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1189,7 +1189,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1203,6 +1203,7 @@ POLARITY <- "NEG"
 data <- filterFile(data_all, which(data_all$polarity == POLARITY))
 hmdb <- hmdb_neg
 hmdb_nl <- hmdb_neg_nl
+csp@tolerance <- 0.01
 ```
 
 ```{r, preprocessing, eval = !file.exists(paste0(RDATA_PATH, "processed_data_", POLARITY, ".RData")), message = FALSE}
@@ -1329,7 +1330,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1396,7 +1397,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1474,7 +1475,7 @@ ms2$confidence <- c("high", "high", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1623,7 +1624,7 @@ ms2$confidence <- c("high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1707,7 +1708,7 @@ ms2$confidence <- c("low", "low", "high", "high", "high", "high",
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1778,7 +1779,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1859,7 +1860,7 @@ ms2$confidence <- c("high", "high", "low", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1935,7 +1936,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Pipecolic acid
@@ -2073,7 +2074,7 @@ ms2$confidence <- c("low", "low", "high", "high", "high", "high",
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -2083,6 +2084,11 @@ ms2$confidence <- c("low", "low", "high", "high", "high", "high",
 
 # Summary on the ion database
 
+Summarizing the content that was added to the `IonDb`.
+
+```{r, iondb-summary, echo = FALSE, results = "asis"}
+```
+
 # Session information
 
 The R version and packages used in this analysis are listed below.
diff --git a/match-standards-serum-mix10.Rmd b/match-standards-serum-mix10.Rmd
index 71391ea..87ee029 100644
--- a/match-standards-serum-mix10.Rmd
+++ b/match-standards-serum-mix10.Rmd
@@ -294,7 +294,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Adenosine
@@ -379,7 +379,7 @@ ms2$confidence <- c("high", "high", "low", "low", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -458,7 +458,7 @@ ms2$confidence <- c("low", "low", "high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Citric Acid
@@ -616,7 +616,7 @@ ms2$confidence <- c("low", "low", "high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -714,7 +714,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Ribulose 5-Phosphate
@@ -810,7 +810,7 @@ ms2$confidence <- c("high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -914,7 +914,7 @@ ms2$confidence <- c("high", "low", "high", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -996,7 +996,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 	
@@ -1166,7 +1166,7 @@ ms2$confidence <- c("low", "low", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### L-Aspartic Acid
@@ -1237,7 +1237,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Citric Acid
@@ -1309,7 +1309,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1390,7 +1390,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### Fumaric Acid
@@ -1469,7 +1469,7 @@ ms2$confidence <- c("low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### GDP
@@ -1619,7 +1619,7 @@ ms2$confidence <- c("low", "high", "high", "high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1697,7 +1697,7 @@ ms2$confidence <- c("low", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1776,7 +1776,7 @@ ms2$confidence <- c("low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1857,7 +1857,7 @@ ms2$confidence <- c("low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ## Standards without any matching feature
@@ -1868,6 +1868,9 @@ ms2$confidence <- c("low", "low")
 
 Summarizing the content that was added to the `IonDb`.
 
+```{r, iondb-summary, echo = FALSE, results = "asis"}
+```
+
 # Session information
 
 The R version and packages used in this analysis are listed below.
diff --git a/match-standards-serum-mix11.Rmd b/match-standards-serum-mix11.Rmd
index 115a845..05d25b5 100644
--- a/match-standards-serum-mix11.Rmd
+++ b/match-standards-serum-mix11.Rmd
@@ -308,7 +308,7 @@ ms2$confidence <- c("high", "high", "high", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### dCTP
@@ -390,7 +390,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -470,7 +470,7 @@ ms2$confidence <- c("high", "low", "low", "low", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -549,7 +549,7 @@ ms2$confidence <- c("low", "low", "low", "low", "high", "high", "high",
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -688,7 +688,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -778,7 +778,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -878,7 +878,7 @@ ms2$confidence <- c("low", "low", "high", "high", "high", "high", "low", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1028,7 +1028,7 @@ ms2$confidence <- c("low", "low", "high", "high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1192,7 +1192,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1257,7 +1257,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 ### dCTP
@@ -1344,7 +1344,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1425,7 +1425,7 @@ ms2$confidence <- c("high")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1496,7 +1496,7 @@ ms2$confidence <- c("low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1598,7 +1598,7 @@ ms2$confidence <- c("high", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1713,7 +1713,7 @@ ms2$confidence <- c("high", "low")
 ```{r, add-ions, echo = FALSE, results = "asis"}
 ```
 
-```{r, add-ms2-spectra, echo = FALSE}
+```{r, add-ms2-spectra, echo = FALSE, results = "asis"}
 ```
 
 
@@ -1778,6 +1778,11 @@ No features.
 
 # Summary on the ion database
 
+Summarizing the content that was added to the `IonDb`.
+
+```{r, iondb-summary, echo = FALSE, results = "asis"}
+```
+
 # Session information
 
 The R version and packages used in this analysis are listed below.