From 89eb288b6bff882d8dcae4b059dc24877bf7bceb Mon Sep 17 00:00:00 2001 From: Akriebs Date: Thu, 18 Apr 2024 10:03:27 -0400 Subject: [PATCH] Amend Vascular Markdown --- docs/Vascular_Slideseq.html | 51 +++++++++++++++++++------------------ 1 file changed, 26 insertions(+), 25 deletions(-) diff --git a/docs/Vascular_Slideseq.html b/docs/Vascular_Slideseq.html index 5d81471..e729be5 100644 --- a/docs/Vascular_Slideseq.html +++ b/docs/Vascular_Slideseq.html @@ -10346,8 +10346,8 @@

Sample BL6J-1

names(rainbow) = levels(voxels_Intensity_1$Bin) voxels_Intensity_1$cols = rainbow[match(voxels_Intensity_1$Bin, names(rainbow))] 
plot3d(voxels_Intensity_1$Voxel_X, voxels_Intensity_1$Voxel_Y, voxels_Intensity_1$Voxel_Z, col = voxels_Intensity_1$cols, add = TRUE)
-
- +
+

Sample BL6J-2

@@ -10361,8 +10361,8 @@

Sample BL6J-2

voxels_Intensity_2$cols = rainbow[match(voxels_Intensity_2$Bin, names(rainbow))] 
close3d()
 plot3d(voxels_Intensity_2$Voxel_X, voxels_Intensity_2$Voxel_Y, voxels_Intensity_2$Voxel_Z, col = voxels_Intensity_2$cols, add = TRUE)
-
- +
+

Sample BL6J-3

@@ -10376,8 +10376,8 @@

Sample BL6J-3

voxels_Intensity_3$cols = rainbow[match(voxels_Intensity_3$Bin, names(rainbow))] 
close3d()
 plot3d(voxels_Intensity_3$Voxel_X, voxels_Intensity_3$Voxel_Y, voxels_Intensity_3$Voxel_Z, col = voxels_Intensity_3$cols, add = TRUE)
-
- +
+
@@ -10452,7 +10452,8 @@

Manhattan Plots

Creating Cell Type Specific Plots

We next examine the spatial distribution of two molecular cell types with a high vascular score, and one molecular cell type with a low -vascular score.

+vascular score. Specifically, for each 100 um voxel, if our cell type of +interest is present, we color that voxel blue.

#Read in the voxelized Slide-seq data
 rctd_reduced = readRDS("Data/Vascular/SupportFiles/100um_Celltypes_in_each_Voxel_and_totalsums.rds")

We first look at the molecular cell type Ex_Sall3_Cd44_2

@@ -10464,24 +10465,24 @@

Cell Type: Ex_Sall3_Cd44_2 Sample: BL6J-1

close3d()
 plot3d(cd44$Voxel_X, cd44$Voxel_Y, cd44$Voxel_Z, col = "blue", add = TRUE)
 plot3d(voxels_Intensity_1$Voxel_X, voxels_Intensity_1$Voxel_Y, voxels_Intensity_1$Voxel_Z, col = voxels_Intensity_1$cols, add = TRUE)
-
- +
+

Cell Type: Ex_Sall3_Cd44_2 Sample: BL6J-2

close3d()
 plot3d(cd44$Voxel_X, cd44$Voxel_Y, cd44$Voxel_Z, col = "blue", add = TRUE)
 plot3d(voxels_Intensity_2$Voxel_X, voxels_Intensity_2$Voxel_Y, voxels_Intensity_2$Voxel_Z, col = voxels_Intensity_2$cols, add = TRUE)
-
- +
+

Cell Type: Ex_Sall3_Cd44_2 Sample: BL6J-3

close3d()
 plot3d(cd44$Voxel_X, cd44$Voxel_Y, cd44$Voxel_Z, col = "blue", add = TRUE)
 plot3d(voxels_Intensity_3$Voxel_X, voxels_Intensity_3$Voxel_Y, voxels_Intensity_3$Voxel_Z, col = voxels_Intensity_3$cols, add = TRUE)
-
- +
+

We next look at the molecular cell type Ex_Fezf2_Il22

celltype = "Ex_Fezf2_Il22"
 fezf2 = rctd_reduced[,c(celltype, "Voxel_X", "Voxel_Y", "Voxel_Z")]
@@ -10492,24 +10493,24 @@ 
Cell Type: Ex_Fezf2_Il22 Sample: BL6J-1

 
close3d()
 plot3d(fezf2$Voxel_X, fezf2$Voxel_Y, fezf2$Voxel_Z, col = "blue", add = TRUE)
 plot3d(voxels_Intensity_1$Voxel_X, voxels_Intensity_1$Voxel_Y, voxels_Intensity_1$Voxel_Z, col = voxels_Intensity_1$cols, add = TRUE)

-

-
+

+

Cell Type: Ex_Fezf2_Il22 Sample: BL6J-2

close3d()
 plot3d(fezf2$Voxel_X, fezf2$Voxel_Y, fezf2$Voxel_Z, col = "blue", add = TRUE)
 plot3d(voxels_Intensity_2$Voxel_X, voxels_Intensity_2$Voxel_Y, voxels_Intensity_2$Voxel_Z, col = voxels_Intensity_2$cols, add = TRUE)
-
- +
+

Cell Type: Ex_Fezf2_Il22 Sample: BL6J-3

close3d()
 plot3d(fezf2$Voxel_X, fezf2$Voxel_Y, fezf2$Voxel_Z, col = "blue", add = TRUE)
 plot3d(voxels_Intensity_3$Voxel_X, voxels_Intensity_3$Voxel_Y, voxels_Intensity_3$Voxel_Z, col = voxels_Intensity_3$cols, add = TRUE)
-
- +
+

Finally, we look at the molecular cell type Ex_Pou4f1_Htr5b_3

celltype = "Ex_Pou4f1_Htr5b_3"
 htr5b = rctd_reduced[,c(celltype, "Voxel_X", "Voxel_Y", "Voxel_Z")]
@@ -10520,24 +10521,24 @@ 
Cell Type: Ex_Pou4f1_Htr5b_3 Sample: BL6J-1

 
close3d()
 plot3d(htr5b$Voxel_X, htr5b$Voxel_Y, htr5b$Voxel_Z, col = "blue", add = TRUE)
 plot3d(voxels_Intensity_1$Voxel_X, voxels_Intensity_1$Voxel_Y, voxels_Intensity_1$Voxel_Z, col = voxels_Intensity_1$cols, add = TRUE)

-

-
+

+

Cell Type: Ex_Pou4f1_Htr5b_3 Sample: BL6J-2

close3d()
 plot3d(htr5b$Voxel_X, htr5b$Voxel_Y, htr5b$Voxel_Z, col = "blue", add = TRUE)
 plot3d(voxels_Intensity_2$Voxel_X, voxels_Intensity_2$Voxel_Y, voxels_Intensity_2$Voxel_Z, col = voxels_Intensity_2$cols, add = TRUE)
-
- +
+

Cell Type: Ex_Pou4f1_Htr5b_3 Sample: BL6J-3

close3d()
 plot3d(htr5b$Voxel_X, htr5b$Voxel_Y, htr5b$Voxel_Z, col = "blue", add = TRUE)
 plot3d(voxels_Intensity_3$Voxel_X, voxels_Intensity_3$Voxel_Y, voxels_Intensity_3$Voxel_Z, col = voxels_Intensity_3$cols, add = TRUE)
-
- +
+