vignettes in bioconductor style in HTML; save intermediary default st…

…yle in markdown
saeyslab · Apr 2, 2024 · 1935d50 · 1935d50
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diff --git a/.DS_Store b/.DS_Store
diff --git a/R/prioritization.R b/R/prioritization.R
@@ -451,7 +451,6 @@ add_extra_criterion = function(prioritization_tables, new_criteria_tbl, regular_
   group_prioritization_tbl = prioritization_tables$group_prioritization_tbl %>% dplyr::mutate(prioritization_score = 0) # because we will recalculate this again
 
   if(scenario == "regular"){
-    #regular_criteria_tbl = regular_criteria_tbl %>% mutate(weight = c(1,1,1,1,1,1,1,1))
     regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_lfc_ligand"] = 1
     regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_p_val_ligand_adapted"] = 1
     regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_lfc_receptor"] = 1
@@ -462,7 +461,6 @@ add_extra_criterion = function(prioritization_tables, new_criteria_tbl, regular_
     regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "fraction_expressing_ligand_receptor"] = 1
   }
   if(scenario == "lower_DE"){
-    #regular_criteria_tbl = regular_criteria_tbl %>% mutate(weight = c(0.5,0.5,0.5,0.5,2,1,1,1))
     regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_lfc_ligand"] = 0.5
     regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_p_val_ligand_adapted"] = 0.5
     regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_lfc_receptor"] = 0.5
@@ -472,6 +470,16 @@ add_extra_criterion = function(prioritization_tables, new_criteria_tbl, regular_
     regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_pb_receptor"] = 1
     regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "fraction_expressing_ligand_receptor"] = 1
   }
+  if(scenario == "no_frac_LR_expr"){
+    regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_lfc_ligand"] = 1
+    regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_p_val_ligand_adapted"] = 1
+    regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_lfc_receptor"] = 1
+    regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_p_val_receptor_adapted"] = 1
+    regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "max_scaled_activity"] = 1
+    regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_pb_ligand"] = 1
+    regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "scaled_pb_receptor"] = 1
+    regular_criteria_tbl$weight[regular_criteria_tbl$criterion == "fraction_expressing_ligand_receptor"] = 0
+  }
 
   criteria_tbl = dplyr::bind_rows(regular_criteria_tbl, new_criteria_tbl)
   # have a weighted average the final score (no product!!)

diff --git a/README.Rmd b/README.Rmd
@@ -83,7 +83,7 @@ TEST
 TEST
 
 * [MultiNicheNet analysis: MIS-C threewise comparison - step-by-step](vignettes/basic_analysis_steps_MISC.html): `vignette("basic_analysis_steps_MISC", package="multinichenetr")`
-* [MultiNicheNet analysis: MIS-C threewise comparison - step-by-step](vignettes/basic_analysis_steps_MISC.md): `vignette("basic_analysis_steps_MISC", package="multinichenetr")`
+* [MultiNicheNet analysis: MIS-C threewise comparison - step-by-step](vignettes/basic_analysis_steps_MISC.knit.md): `vignette("basic_analysis_steps_MISC", package="multinichenetr")`
 
 TEST 
 TEST

diff --git a/README.md b/README.md
@@ -138,7 +138,7 @@ TEST TEST TEST TEST
     step-by-step](vignettes/basic_analysis_steps_MISC.html):
     `vignette("basic_analysis_steps_MISC", package="multinichenetr")`
 -   [MultiNicheNet analysis: MIS-C threewise comparison -
-    step-by-step](vignettes/basic_analysis_steps_MISC.md):
+    step-by-step](vignettes/basic_analysis_steps_MISC.knit.md):
     `vignette("basic_analysis_steps_MISC", package="multinichenetr")`
 
 TEST TEST TEST TEST

diff --git a/vignettes/.DS_Store b/vignettes/.DS_Store
diff --git a/vignettes/basic_analysis_steps_MISC.Rmd b/vignettes/basic_analysis_steps_MISC.Rmd
@@ -17,6 +17,10 @@ vignette: >
 }
 </style>
 
+<!-- github markdown built using
+rmarkdown::render("vignettes/basic_analysis_steps_MISC.Rmd", clean = FALSE )
+-->
+
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -27,10 +31,6 @@ knitr::opts_chunk$set(
 library(BiocStyle)
 ```
 
-<!-- github markdown built using
-rmarkdown::render("vignettes/basic_analysis_steps_MISC.Rmd",output_format = "md_document")
--->
-
 In this vignette, you can learn how to perform a MultiNicheNet analysis to compare cell-cell communication between conditions of interest. A MultiNicheNet analysis can be performed if you have multi-sample, multi-condition/group single-cell data. We strongly recommend having at least 4 samples in each of the groups/conditions you want to compare. With less samples, the benefits of performing a pseudobulk-based DE analysis are less clear. For those datasets, you can check and run our alternative workflow that makes use of cell-level sample-agnostic differential expression tools.
 
 As input you need a SingleCellExperiment object containing at least the raw count matrix and metadata providing the following information for each cell: the **group**, **sample** and **cell type**.

diff --git a/vignettes/basic_analysis_steps_MISC.html b/vignettes/basic_analysis_steps_MISC.html
diff --git a/vignettes/basic_analysis_steps_MISC.knit.md b/vignettes/basic_analysis_steps_MISC.knit.md
diff --git a/vignettes/basic_analysis_steps_MISC_SACL.Rmd b/vignettes/basic_analysis_steps_MISC_SACL.Rmd
@@ -16,6 +16,10 @@ vignette: >
 }
 </style>
 
+<!-- github markdown built using
+rmarkdown::render("vignettes/basic_analysis_steps_MISC.Rmd", clean = FALSE )
+-->
+
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,

diff --git a/vignettes/basic_analysis_steps_MISC_files/.DS_Store b/vignettes/basic_analysis_steps_MISC_files/.DS_Store
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-Original file line number
+Diff line change
@@ Expand Up / @@ -83,7 +83,7 @@ TEST @@
     TEST
     * [MultiNicheNet analysis: MIS-C threewise comparison - step-by-step](vignettes/basic_analysis_steps_MISC.html): `vignette("basic_analysis_steps_MISC", package="multinichenetr")`
-    * [MultiNicheNet analysis: MIS-C threewise comparison - step-by-step](vignettes/basic_analysis_steps_MISC.md): `vignette("basic_analysis_steps_MISC", package="multinichenetr")`
+    * [MultiNicheNet analysis: MIS-C threewise comparison - step-by-step](vignettes/basic_analysis_steps_MISC.knit.md): `vignette("basic_analysis_steps_MISC", package="multinichenetr")`
     TEST
     TEST
@@ Expand Down @@