add rshiny app

Author: mhurtado13

DESCRIPTION

@@ -69,7 +69,9 @@ Suggests:
     MCPcounter (>= 1.2.0),
     knitr,
     matlib,
-    rmarkdown
+    rmarkdown,
+    shiny,
+    pkgload
 LazyData: true
 LazyDataCompression: bzip2
 Config/testthat/edition: 3

R/cell_deconvolution.R

@@ -121,7 +121,7 @@ standardize_celltype_colnames <- function(mat) {
 
   ## CD4 and subtypes
   lower <- stringr::str_to_lower(colnames(mat))
-  is_cd4 <- grepl("\\bcd4\\b", lower)
+  is_cd4 <- grepl("\\bcd4\\b|reg|regulatory", lower)
   is_tcell_variant <- grepl("(^|[^a-z0-9])(t|tcell|t\\.cells|t_cells|t cells)([^a-z0-9]|$)", lower, perl = TRUE)
   is_memory <- grepl("memory", lower)
   cd4_idx <- which(is_cd4 | (is_tcell_variant & is_memory))
@@ -170,15 +170,15 @@ standardize_celltype_colnames <- function(mat) {
     colnames(blocks$CD4.non.regulatory) <- stringr::str_replace(
       colnames(blocks$CD4.non.regulatory),
       "(?i)^(.*?)(?:_)?(T[_\\.-]?cell[_\\.-]?CD4[_\\.-]?.*non[._-]?regulatory.*|T[_\\.-]?cells?[_\\.-]?.*non[._-]?regulatory.*|CD4[_\\.-]?non[._-]?regulatory.*|T\\.cells\\.non\\.regulatory|T_cells_non_regulatory|nonregulatory|non[\\W_]?reg)$",
-      "\\1_CD4.non.regulatory"
+      "CD4.non.regulatory"
     )
   }
   if (ncol(blocks$CD4.regulatory)){
     mat <- mat[, !colnames(mat) %in% colnames(blocks$CD4.regulatory), drop = FALSE]
     colnames(blocks$CD4.regulatory) <- stringr::str_replace(
       colnames(blocks$CD4.regulatory),
       "(?i)^(.*?)(?:_)?(T[_\\.-]?cell[_\\.-]?regulatory.*|T[_\\.-]?cells?[_\\.-]?regulatory.*|T\\.cells\\.regulatory.*|tregs?\\.?$|tregulatory.*|regulatory.*)$",
-      "\\1_CD4.regulatory"
+      "CD4.regulatory"
     )
   }
 
@@ -2987,6 +2987,21 @@ create_gsea_signature <- function(gene_scores,
   pos <- fg %>% 
     dplyr::filter(!is.na(NES) & NES > 0) %>%  # Keep positive NES
     dplyr::arrange(dplyr::desc(NES)) # Arrange by descending NES
+
+  #fg_top <- fg %>%
+  #  dplyr::filter(!is.na(NES)) %>%
+  #  dplyr::arrange(dplyr::desc(dplyr::abs(NES))) %>%
+  #  dplyr::slice_head(n = 20) %>%
+  #  dplyr::mutate(pathway = factor(pathway, levels = rev(pathway)),
+  #                sig = -log10(padj + 1e-300))
+
+  #ggplot(fg_top, aes(x = NES, y = pathway, size = size, color = sig)) +
+  #  geom_point() +
+  #  scale_color_viridis_c(name = "-log10(padj)") +
+  #  scale_size_continuous(name = "pathway size") +
+  #  labs(title = "FGSEA — top 20 pathways", x = "NES", y = NULL) +
+  #  theme_minimal(base_size = 12)
+  
   if (nrow(pos) == 0) stop("No pathways with NES > 0 found")
   first_pathway <- as.character(pos$pathway[1]) 
   suffix <- stringr::str_replace_all(first_pathway, "[^A-Za-z0-9]+", "_") # Replace non-alphanumeric characters with underscores
@@ -3009,7 +3024,7 @@ expand_subgroup_members <- function(subgroup, subgroup_map) {
 }
 
 
-compute_deconvolution_dictionary <- function(subgroups, expr) {
+compute_deconvolution_dictionary <- function(subgroups, expr, pathways = NULL) {
 
   subgroup_map <- subgroups[["Deconvolution subgroups composition"]]
   deconv_mat = subgroups[["Deconvolution matrix"]]
@@ -3029,7 +3044,7 @@ compute_deconvolution_dictionary <- function(subgroups, expr) {
                                          deconv = deconv_mat,
                                          subgroup = sub_name) # Compute correlation rankings for the subgroup
 
-      sig_out <- create_gsea_signature(ranked, sub_name) # create pathwyas signature
+      sig_out <- create_gsea_signature(ranked, sub_name, pathways) # create pathwyas signature
       if (is.null(sig_out)) next # No enrichment found, skip to next subgroup
       new_label <- sig_out[[1]]
       idx <- which(colnames(deconv_mat) == sub_name) # replace column name in deconv_mat if present
@@ -3047,21 +3062,3 @@ compute_deconvolution_dictionary <- function(subgroups, expr) {
 
   return(subgroups)
 }
-
-library(ggplot2)
-library(dplyr)
-library(viridis)
-# FGSEA dotplot (top 20 by |NES|)
-fg_top <- fgseaRes |>
-  filter(!is.na(NES)) |>
-  arrange(desc(abs(NES))) |>
-  slice_head(n = 20) |>
-  mutate(pathway = factor(pathway, levels = rev(pathway)),
-         sig = -log10(padj + 1e-300))
-
-ggplot(fg_top, aes(x = NES, y = pathway, size = size, color = sig)) +
-  geom_point() +
-  scale_color_viridis_c(name = "-log10(padj)") +
-  scale_size_continuous(name = "pathway size") +
-  labs(title = "FGSEA — top 20 pathways", x = "NES", y = NULL) +
-  theme_minimal(base_size = 12)

README.Rmd

@@ -90,6 +90,33 @@ Users can also compute second-generation deconvolution methods using their singl
 deconv_sc = compute_sc_deconvolution_methods(raw_counts, sc_object, sc_metadata, cell_annotations, samples_ids, name_object, normalized = T, n_cores = 4, cbsx_name = "XXX", cbsx_token = "XXX")
 ```
 
+## Shiny app
+
+`multideconv` includes an interactive Shiny app for non-coding users with four tabs: **Welcome**, **Deconvolution**, **Analysis**, and **Benchmark**.
+
+From the repository root, run:
+
+``` bash
+Rscript -e "shiny::runApp('inst/shiny', host='127.0.0.1', port=3838, launch.browser=TRUE)"
+```
+
+Or from an R session:
+
+``` r
+setwd("~/path/to/multideconv")
+shiny::runApp("inst/shiny", host = "127.0.0.1", port = 3838, launch.browser = TRUE)
+```
+
+If port `3838` is already in use, choose another one (for example `3840`) and open:
+
+`http://127.0.0.1:3840`
+
+You can stop old Shiny processes with:
+
+``` bash
+pkill -f "shiny::runApp\\('inst/shiny'"
+```
+
 ## Cell types nomenclature
 
 `multideconv` works based on established cell naming conventions (Figure 2) to simplify analysis and processing. Thus, if you would like to use your own deconvolution results or signatures, please make sure to follow these formats.

README.md

@@ -106,6 +106,36 @@ already included in `compute.deconvolution` when setting
 deconv_sc = compute_sc_deconvolution_methods(raw_counts, sc_object, sc_metadata, cell_annotations, samples_ids, name_object, normalized = T, n_cores = 4, cbsx_name = "XXX", cbsx_token = "XXX")
 ```
 
+## Shiny app
+
+`multideconv` includes an interactive Shiny app for non-coding users with
+four tabs: **Welcome**, **Deconvolution**, **Analysis**, and
+**Benchmark**.
+
+From the repository root, run:
+
+``` bash
+Rscript -e "shiny::runApp('inst/shiny', host='127.0.0.1', port=3838, launch.browser=TRUE)"
+```
+
+Or from an R session:
+
+``` r
+setwd("~/path/to/multideconv")
+shiny::runApp("inst/shiny", host = "127.0.0.1", port = 3838, launch.browser = TRUE)
+```
+
+If port `3838` is already in use, choose another one (for example
+`3840`) and open:
+
+`http://127.0.0.1:3840`
+
+You can stop old Shiny processes with:
+
+``` bash
+pkill -f "shiny::runApp\\('inst/shiny'"
+```
+
 ## Cell types nomenclature
 
 `multideconv` works based on established cell naming conventions (Figure

inst/shiny/README.md

@@ -0,0 +1,19 @@
+# multideconv Shiny app
+
+This app exposes the main multideconv workflows from the package source and vignette:
+
+1. `compute.deconvolution`
+2. `compute.deconvolution.analysis`
+3. `compute.benchmark`
+
+It includes built-in example datasets and file upload options.
+
+## Run
+
+From the repository root:
+
+```r
+shiny::runApp("inst/shiny")
+```
+
+If `multideconv` is not installed, the app tries to load the package from source using `pkgload::load_all()`.