update tma and split_join

drieslab · Nov 14, 2024 · 9474ebc · 9474ebc
1 parent 1393c74
commit 9474ebc
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Showing 14 changed files with 272 additions and 184 deletions.
diff --git a/vignettes/images/split_join/1_align_a.png b/vignettes/images/split_join/1_align_a.png
diff --git a/vignettes/images/split_join/2_align_b.png b/vignettes/images/split_join/2_align_b.png
diff --git a/vignettes/images/split_join/3_join_dry.png b/vignettes/images/split_join/3_join_dry.png
diff --git a/vignettes/images/split_join/4_join_dry_specific.png b/vignettes/images/split_join/4_join_dry_specific.png
diff --git a/vignettes/images/split_join/5_join_shift.png b/vignettes/images/split_join/5_join_shift.png
diff --git a/vignettes/images/split_join/6_join_stack.png b/vignettes/images/split_join/6_join_stack.png
diff --git a/vignettes/images/split_join/7_join_nc.png b/vignettes/images/split_join/7_join_nc.png
diff --git a/vignettes/images/split_join/1_spatplot.png → vignettes/images/tma/1_spatplot.png b/vignettes/images/split_join/1_spatplot.png → vignettes/images/tma/1_spatplot.png
diff --git a/...ttes/images/split_join/2_identify_tma.png → vignettes/images/tma/2_identify_tma.png b/...ttes/images/split_join/2_identify_tma.png → vignettes/images/tma/2_identify_tma.png
diff --git a/vignettes/images/split_join/3_annotated.png → vignettes/images/tma/3_annotated.png b/vignettes/images/split_join/3_annotated.png → vignettes/images/tma/3_annotated.png
diff --git a/...ettes/images/split_join/4_lung_joined.png → vignettes/images/tma/4_lung_joined.png b/...ettes/images/split_join/4_lung_joined.png → vignettes/images/tma/4_lung_joined.png
diff --git a/...ttes/images/split_join/5_brain_joined.png → vignettes/images/tma/5_brain_joined.png b/...ttes/images/split_join/5_brain_joined.png → vignettes/images/tma/5_brain_joined.png
diff --git a/vignettes/split_join.Rmd b/vignettes/split_join.Rmd
diff --git a/vignettes/tma.Rmd b/vignettes/tma.Rmd
@@ -89,7 +89,7 @@ spatPlot2D(tma, show_image = TRUE, point_size = 1.5, point_alpha = 0.7)
 ```
 
 ```{r, echo=FALSE, out.width="100%", fig.align="center"}
-knitr::include_graphics("images/split_join/1_spatplot.png")
+knitr::include_graphics("images/tma/1_spatplot.png")
 ```
 
 ## Detect individual TMA cores
@@ -116,7 +116,7 @@ spatPlot2D(tma,
 ```
 
 ```{r, echo=FALSE, out.width="100%", fig.align="center"}
-knitr::include_graphics("images/split_join/2_identify_tma.png")
+knitr::include_graphics("images/tma/2_identify_tma.png")
 ```
 
 The cores have been assigned numerical IDs. There is also a `"not_connected"`
@@ -153,7 +153,7 @@ spatPlot2D(tma,
 ```
 
 ```{r, echo=FALSE, out.width="100%", fig.align="center"}
-knitr::include_graphics("images/split_join/3_annotated.png")
+knitr::include_graphics("images/tma/3_annotated.png")
 ```
 
 
@@ -214,7 +214,7 @@ spatPlot2D(lung,
 
 
 ```{r, echo=FALSE, out.width="100%", fig.align="center"}
-knitr::include_graphics("images/split_join/4_lung_joined.png")
+knitr::include_graphics("images/tma/4_lung_joined.png")
 ```
 
 ```{r, eval=FALSE}
@@ -237,7 +237,7 @@ spatPlot2D(brain,
 ```
 
 ```{r, echo=FALSE, out.width="80%", fig.align="center"}
-knitr::include_graphics("images/split_join/5_brain_joined.png")
+knitr::include_graphics("images/tma/5_brain_joined.png")
 ```