Add diffexp and diffadb projections to plot_features (#26)

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gedi2
 Type: Package
 Title: Gene Expression Decomposition and Integration
-Version: 2.3.4
-Date: 2026-05-09
+Version: 2.3.5
+Date: 2026-06-09
 Authors@R: c(
     person("Arsham", "Mikaeili Namini", email = "arsham.mikaeilinamini@mail.mcgill.ca", role = c("aut", "cre")),
     person("Hamed", "S.Najafabadi", email = "hamed.najafabadi@mcgill.ca", role = c("aut"))

NEWS.md

@@ -1,3 +1,18 @@
+# gedi 2.3.5
+
+## New features
+
+* `plot_features()` gains two differential projection types (#26):
+  * `projection = "diffexp"` plots the per-cell differential expression for
+    selected genes, given a `contrast` (optionally adding the global offset via
+    `include_O = TRUE`). The full J x N matrix is never materialised.
+  * `projection = "diffadb"` plots the per-cell differential pathway activity
+    for selected pathways (requires a gene-level prior `C`).
+* New method `model$diffADB(contrast)` returns the differential pathway
+  activity (num_pathways x N). It is the exact differential of `ADB`
+  (i.e. `ADB(Z + dQ) - ADB(Z)`), applying the same `solve_A` shrinkage so it
+  stays on the same scale as `model$projections$ADB`.
+
 # gedi 2.3.1
 
 ## CRAN Compliance

R/RcppExports.R

@@ -208,6 +208,10 @@ getDiffExp_cpp <- function(Rk_list, H_rotation, contrast, D, Bi_list, verbose =
     .Call(`_gedi2_getDiffExp_cpp`, Rk_list, H_rotation, contrast, D, Bi_list, verbose)
 }
 
+getDiffADB_cpp <- function(Rk_list, H_rotation, contrast, C_rotation, inputC, D, Bi_list, S_A, verbose = 0L) {
+    .Call(`_gedi2_getDiffADB_cpp`, Rk_list, H_rotation, contrast, C_rotation, inputC, D, Bi_list, S_A, verbose)
+}
+
 compute_svd_factorized_cpp <- function(Z, D, Bi_list, verbose = 0L) {
     .Call(`_gedi2_compute_svd_factorized_cpp`, Z, D, Bi_list, verbose)
 }

R/gedi_class.R

@@ -697,6 +697,9 @@ GEDI <- R6Class(
     diffExp = function(contrast, include_O = FALSE) {
       compute_diffExp(self, private, contrast, include_O)
     },
+    diffADB = function(contrast) {
+      compute_diffADB(self, private, contrast)
+    },
 
     # =========================================================================
     # Dimensionality Reduction Methods