From 16351ecf6643bfb7f2ccf70c8808cb483006f3be Mon Sep 17 00:00:00 2001
From: Yichen Wang <wayichen@umich.edu>
Date: Tue, 11 Jun 2024 14:44:49 -0400
Subject: [PATCH] Allow tryCatch when pseudo-bulk does not work with small
 clusters

---
 R/DEG_marker.R    | 28 ++++++++++++++++++++++++----
 R/visualization.R | 14 ++++++++------
 2 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/R/DEG_marker.R b/R/DEG_marker.R
index ea49715..f148e88 100644
--- a/R/DEG_marker.R
+++ b/R/DEG_marker.R
@@ -185,13 +185,33 @@ runMarkerDEG <- function(
     } else {
         result <- list()
         for (i in seq_along(levels(splitBy))) {
+            if (isTRUE(verbose)) {
+                cli::cli_alert_info(
+                    "Running psuedo-bulk DEG on: {.val {levels(splitBy)[i]}}"
+                )
+            }
+
             subIdx <- splitBy == levels(splitBy)[i]
             subCellIdx <- allCellIdx[subIdx]
             groups <- split(subCellIdx, conditionBy[subIdx])
-            result[[levels(splitBy)[i]]] <- .runDEG(
-                object, groups = groups, method = method, usePeak = usePeak,
-                useReplicate = useReplicate, nPsdRep = nPsdRep,
-                minCellPerRep = minCellPerRep, seed = seed, verbose = verbose
+            result[[levels(splitBy)[i]]] <- tryCatch(
+                {
+                    .runDEG(
+                        object, groups = groups, method = method,
+                        usePeak = usePeak, useReplicate = useReplicate,
+                        nPsdRep = nPsdRep, minCellPerRep = minCellPerRep,
+                        seed = seed, verbose = verbose
+                    )
+                },
+                error = function(e) {
+                    cli::cli_alert_danger(
+                        "Error when computing on {.val {levels(splitBy)[i]}}: {e$message}"
+                    )
+                    cli::cli_alert_warning(
+                        "Empty result (NULL) returned for this test."
+                    )
+                    return(NULL)
+                }
             )
         }
     }
diff --git a/R/visualization.R b/R/visualization.R
index f9a10b8..d0cbeaa 100644
--- a/R/visualization.R
+++ b/R/visualization.R
@@ -702,12 +702,12 @@ plotProportionBox <- function(
                             fill = .data[[conditionBy]]
                         )
                     else ggplot2::aes(
-                        x = .data[[conditionBy]],
+                        x = .data[[useCluster]],
                         y = .data[["Proportion"]]
                     )
                 )
-            ) +
-                (if (isTRUE(dot))
+            ) + (
+                if (isTRUE(dot))
                     ggplot2::geom_point(
                         size = dotSize,
                         color = "black",
@@ -715,9 +715,11 @@ plotProportionBox <- function(
                             if (isTRUE(dotJitter)) ggplot2::position_jitter()
                         else "identity"
                     )
-                 else
-                     NULL) +
-                ggplot2::geom_boxplot()
+                else
+                    NULL
+            ) +
+                ggplot2::geom_boxplot() +
+                ggplot2::ggtitle(paste0(useCluster, ": ", cluster))
             return(.ggplotLigerTheme(p, ...))
         })
         names(plist) <- levels(clusterVar)