From a61a6bda4676a33d93224134154c2fb187770bd1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Thu, 26 Jan 2023 19:05:11 +0100
Subject: [PATCH] app: app_config_and_status, inputs_metfrag
* app_config_and_status: Updated. Replaced metfrag controls with inject_inputs.
---
R/inputs_metfrag.R | 4 +++
inst/rmd/app_config_and_status.Rmd | 56 +++++++-----------------------
2 files changed, 16 insertions(+), 44 deletions(-)
diff --git a/R/inputs_metfrag.R b/R/inputs_metfrag.R
index 4d84051..7423493 100644
--- a/R/inputs_metfrag.R
+++ b/R/inputs_metfrag.R
@@ -6,6 +6,10 @@ mk_shiny_control <- function(name,fun,args) {
res
}
+inject_inputs<- function(collection,which) {
+ do.call(shiny::tagList,lapply(which,function(nm) collection[[nm]]$content))
+}
+
INPUTS_METFRAG_NUMERIC = list(mk_shiny_control(name="mf_database_search_relative_mass_deviation",
fun="numericInput",
args=list(label="Database search relative mass deviation",
diff --git a/inst/rmd/app_config_and_status.Rmd b/inst/rmd/app_config_and_status.Rmd
index 8e4229b..f739771 100644
--- a/inst/rmd/app_config_and_status.Rmd
+++ b/inst/rmd/app_config_and_status.Rmd
@@ -159,17 +159,9 @@ shinyscreen::rt_input(input_rt = "ret_time_shift_tol",
#### Tolerance and Tree Depth Controls
```{r, echo=F}
-numericInput("mf_database_search_relative_mass_deviation",
- label="Database search relative mass deviation",
- value=5)
-numericInput("mf_fragment_peak_match_absolute_mass_deviation",
- label="Fragment peak match absolute mass deviation",
- value=METFRAG_DEFAULT_ABSMASSDEV)
-numericInput("mf_fragment_peak_match_relative_mass_deviation",
- label="Fragment peak match relative mass deviation",
- value=METFRAG_DEFAULT_RELMASSDEV)
-numericInput("mf_maximum_tree_depth", label="MaximumTreeDepth",
- value=METFRAG_DEFAULT_MAX_TREE_DEPTH)
+inject_inputs(INPUTS_METFRAG,c("mf_fragment_peak_match_absolute_mass_deviation",
+ "mf_fragment_peak_match_relative_mass_deviation",
+ "mf_maximum_tree_depth"))
```
</div> <!-- metfrag-conf-tolerance -->
@@ -178,20 +170,9 @@ numericInput("mf_maximum_tree_depth", label="MaximumTreeDepth",
#### Processing
```{r, echo=F}
-selectInput("mf_pre_processing_candidate_filter",
- label="Preprocessing candidate filter",
- choices=shinyscreen:::METFRAG_PREPFLT_CHOICES,
- selected=shinyscreen:::METFRAG_PREPFLT_DEFAULT,
- multiple=T)
-selectInput("mf_post_processing_candidate_filter",
- label="Postprocessing candidate filter",
- choices=shinyscreen:::METFRAG_POSTPFLT_CHOICES,
- selected=shinyscreen:::METFRAG_POSTPFLT_DEFAULT,
- multiple=T)
-selectInput("mf_metfrag_candidate_writer",
- label="MetFrag Candidate Writer",
- choices=shinyscreen:::METFRAG_WRITER_CHOICES,
- selected=shinyscreen:::METFRAG_DEFAULT_WRITER)
+inject_inputs(INPUTS_METFRAG,c("mf_pre_processing_candidate_filter",
+ "mf_post_processing_candidate_filter",
+ "mf_metfrag_candidate_writer"))
```
</div> <!-- metfrag-conf-processing -->
@@ -203,16 +184,10 @@ selectInput("mf_metfrag_candidate_writer",
#### Databases
```{r, echo=F}
-selectInput("mf_database_type", label="Database type",
- choices=METFRAG_DATABASE_TYPE,
- selected=METFRAG_DEFAULT_DATABASE_TYPE)
-selectInput("mf_local_database",
- label="Local Database",
- choices=character(0))
-selectInput("mf_local_db_col_ident",
- label="Select Identifiers",
- multiple = T,
- choices=character(0))
+inject_inputs(INPUTS_METFRAG,c("mf_database_type",
+ "mf_local_database",
+ "mf_local_db_col_ident",
+ "mf_local_db_col_coll"))
```
</div> <!-- metfrag-conf-databases -->
@@ -222,11 +197,7 @@ selectInput("mf_local_db_col_ident",
#### MetFrag Scores
```{r, echo = F}
-selectInput("mf_scores_intrinsic",
- label="Select Scoring Types",
- choices = METFRAG_INTRINSIC_SCORES,
- multiple = T,
- selected = names(METFRAG_DEFAULT_SCORES))
+inject_inputs(INPUTS_METFRAG,"mf_scores_intrinsic")
DT::DTOutput("mf_local_ident")
```
@@ -236,10 +207,7 @@ DT::DTOutput("mf_local_ident")
#### Local Database Scoring Terms
```{r, echo = F}
-selectInput("mf_local_db_col_scores",
- label="Select local scoring terms",
- multiple = T,
- choices=character(0))
+inject_inputs(INPUTS_METFRAG,"mf_local_db_col_scores")
DT::DTOutput("mf_local_db_scores")
```
--
GitLab