diff --git a/02_session3.Rmd b/02_session3.Rmd index a4081f6..bfc55be 100644 --- a/02_session3.Rmd +++ b/02_session3.Rmd @@ -492,15 +492,15 @@ These transforms are normally done automatically when using: ``` # convenience function params load_images = list( -img1 = "[img_path1.tif]", -img2 = "[img_path2.tif]", -img3 = "..." + img1 = "[img_path1.tif]", + img2 = "[img_path2.tif]", + img3 = "..." ), load_aligned_images = list( -aligned_img = c( -"[path to image.tif]", -"[path to magealignment.csv]" -) + aligned_img = c( + "[path to image.tif]", + "[path to magealignment.csv]" + ) ) # importer params @@ -508,9 +508,9 @@ x$load_image(path = "[img_path1.tif]", name = "img1") x$load_image(path = "[img_path2.tif]", name = "img2") ... x$load_aligned_image( -path = "[path to image.tif]", -imagealignment_path = "[path to magealignment.csv]", -name = "aligned_img" + path = "[path to image.tif]", + imagealignment_path = "[path to magealignment.csv]", + name = "aligned_img" ) ``` @@ -947,7 +947,7 @@ knitr::include_graphics("img/02_session3/cc_enrich2.png") Another thing we can do is create a "pseudovisium" dataset by tessellating across this dataset using the same layout and resolution as a Visium capture array. -`makePseudoVisium` generates a Visium array of circular polygons across the spatial extent provided. +`makePseudoVisium()` generates a Visium array of circular polygons across the spatial extent provided. Here we use `ext()` with the `prefer` arg pointing to the polygon and points data and `all_data = TRUE`, meaning that the combined spatial extent of those two data types will be returned, giving a good measure of where all the data in the object is at the moment.