+contrasts/saturation examples

HelenaLC · Nov 25, 2024 · 683ea42 · 683ea42
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diff --git a/vignettes/SpatialData.plot.Rmd b/vignettes/SpatialData.plot.Rmd
@@ -279,12 +279,32 @@ x <- readSpatialData(pa, anndataR=FALSE)
 Plotting with multiple image channels.
 
 ```{r steinbock-plot}
-plotSpatialData() + plotImage(x, 
+plotSpatialData() + plotImage(x,
     i="Patient3_003_image",
     ch=c(6, 22, 39),
     c=c("blue", "cyan", "yellow"))
 ```
 
+### aesthetics
+
+```{r saturation, fig.width=9, fig.height=3}
+p <- plotSpatialData()
+i <- image(x, "Patient3_003_image")
+image(x, "crop") <- i[, 200:400, 200:400]
+lapply(c(1, 0.7, 0.4), \(.) {
+    p + plotImage(x, "crop", sat=c(1.4, 1.2, .), 
+        ch=c(6, 22, 39), c=c("blue", "cyan", "yellow"))
+}) |> wrap_plots(nrow=1)
+```
+
+```{r contrasts, fig.width=9, fig.height=3}
+lapply(list(c(0, 1), c(0.2, 1), c(0, 0.8)), \(.) {
+    p + plotImage(x, "crop", 
+        lim=list(c(0, 1), c(0, 1), .),
+        ch=c(6, 22, 39), c=c("blue", "cyan", "yellow"))
+}) |> wrap_plots(nrow=1)
+```
+
 # Masking
 
 Back to blobs...