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CostaLab · Jul 1, 2024 · 66ca809 · 66ca809
1 parent 6ab3a60
commit 66ca809
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Showing 4 changed files with 8 additions and 13 deletions.
diff --git a/.github/workflows/render-rmarkdown.yaml b/.github/workflows/render-rmarkdown.yaml
@@ -51,7 +51,7 @@ jobs:
       #   shell: Rscript {0}
       - name: Render Rmarkdown files
         run : |
-          pkgdown::build_article(name='myofibroblast-GRN', quiet=FALSE)
+          pkgdown::build_article(name='install.Rmd', quiet=FALSE)
         shell: Rscript {0}
       - name: Commit files
         run: |

diff --git a/R/grn.R b/R/grn.R
@@ -450,10 +450,7 @@ GRNPlot <- function(df.grn,
 GRNSpatialPlot <- function(object, assay,
                            df.grn,
                            tf.use,
-                           min.cutoff = "q5",
-                           max.cutoff = "q95",
-                          vis.option = "B",
-                          crop = TRUE){
+                           vis.option = "B", ...){
     DefaultAssay(object) <- assay
 
     # select all targets for a TF
@@ -462,10 +459,7 @@ GRNSpatialPlot <- function(object, assay,
     geneset <- list(tf.use = df.target$gene)
     object <- AddModuleScore(object, features = geneset)
 
-    p <- Seurat::SpatialFeaturePlot(object, features = "Cluster1",
-                         min.cutoff = min.cutoff,
-                         max.cutoff = max.cutoff,
-                         crop = crop)+
+    p <- Seurat::SpatialFeaturePlot(object, features = "Cluster1", ...)+
             scale_fill_viridis(option = vis.option) +
             ggtitle(glue::glue("{tf.use} targets")) +
     labs(fill='')

diff --git a/run.sh b/run.sh
@@ -2,4 +2,4 @@
 
 # R -e "devtools::document()"
 # R -e "pkgdown::build_site(preview = FALSE, lazy=TRUE)"
-R -e "pkgdown::build_article(name='myofibroblast-GRN', quiet=FALSE)"
+# R -e "pkgdown::build_article(name='myofibroblast-GRN', quiet=FALSE)"
diff --git a/vignettes/myofibroblast-GRN.Rmd b/vignettes/myofibroblast-GRN.Rmd
@@ -578,7 +578,8 @@ obj.spatial <- readRDS("./VisiumSpatial/AKK004_157772.rds")
 DefaultAssay(obj.spatial) <- "c2l_props"
 
 p <- SpatialFeaturePlot(obj.spatial, features = "Fib", min.cutoff = "q5",
-                       max.cutoff = "q95") +
+                       max.cutoff = "q95", image.alpha = 1, 
+                       pt.size.factor = 400, keep.scale = NULL) +
     scale_fill_viridis(option = "D") +
     ggtitle("") +
     labs(fill = "") +
@@ -593,12 +594,12 @@ We next can check the gene expression in space. Here, we use the above TFs.
 ```{r, fig.height = 5, fig.width = 10, fig.align = "center", eval=TRUE}
 DefaultAssay(obj.spatial) <- "SCT"
 
-p1 <- SpatialFeaturePlot(object = obj.spatial, features = "NR3C2") +
+p1 <- SpatialFeaturePlot(object = obj.spatial, features = "NR3C2", image.alpha = 1, pt.size.factor = 400, keep.scale = NULL) +
     ggtitle("") +
     theme(legend.position = "bottom") +
 scale_fill_viridis(option = "C")
 
-p2 <- SpatialFeaturePlot(object = obj.spatial, features = "RUNX1") +
+p2 <- SpatialFeaturePlot(object = obj.spatial, features = "RUNX1", image.alpha = 1, pt.size.factor = 400, keep.scale = NULL) +
     ggtitle("") +
     theme(legend.position = "bottom") +
 scale_fill_viridis(option = "C")