舊號無故被封，小號再發一次
更多空間轉錄組文章：
1. 新版10X Visium
- 【10X空間轉錄組Visium】（一）Space Ranger 1.0.0(更新于20191205）
- 【10X空間轉錄組Visium】（二）Loupe Browser 4.0.0
- 【10X空間轉錄組Visium】（三）跑通Visium全流程記錄
- 【10X空間轉錄組Visium】（四）R下游分析的探索性代碼示例
- 【10X空間轉錄組Visium】（五）Visium原理、流程與產品
- 【10X空間轉錄組Visium】（六）新版Seurat v3.2分析Visium空間轉錄組結果的代碼實操
- 【10X空間轉錄組Visium】（七）思考新版Seurat V3.2作者在Github給予的回答
2. 舊版Sptial
- 【舊版空間轉錄組Spatial】（一）ST Spot Detector使用指南
- 【舊版空間轉錄組Spatial】（二）跑通流程試驗記錄
- 【舊版空間轉錄組Spatial】（三）ST Spot Detector實操記錄
問題描述：
在對自己跑出來的空間轉錄組數據用Seurat V3.2進行分析時取子集遇到一個問題，我不知道該如何選取像素點坐標，以及用官網給的字段會出現報錯的情況，于是我在Github上作者大神提問，不出意外，下面也有一個跟我遇到的情況類似的。
github issue地址：https://github.com/satijalab/seurat/issues/2454
提問原文（biejiaodeyingwen）
Hi~I meet some problem in Subset out anatomical regions
I use the dataset: Mouse Brain Section (Coronal), and run sapceranger successfully,and get clustering_visualization img.
#Subset out anatomical regions
cortex <- subset(brain, idents = c(0, 1, 2, 5, 10, 11, 12 ))
# now remove additional cells, use SpatialDimPlots to visualize what to remove
# SpatialDimPlot(cortex,cells.highlight = WhichCells(cortex, expression = image_imagerow > 400 |
# image_imagecol < 150))
cortex <- subset(cortex, imgine_imagerow > 400 | image_imagecol < 150, invert = TRUE)
cortex <- subset(cortex, image_imagerow > 275 & image_imagecol > 370, invert = TRUE)
cortex <- subset(cortex, image_imagerow > 250 & image_imagecol > 440, invert = TRUE)
then, the error occur:
> #Subset out anatomical regions
> cortex <- subset(brain, idents = c(0, 1, 2, 5, 10, 11, 12 ))
> # now remove additional cells, use SpatialDimPlots to visualize what to remove
> # SpatialDimPlot(cortex,cells.highlight = WhichCells(cortex, expression = image_imagerow > 400 |
> # image_imagecol < 150))
> cortex <- subset(cortex, imgine_imagerow > 400 | image_imagecol < 150, invert = TRUE)
Error in FetchData(object = object, vars = expr.char[vars.use], cells = cells, :
None of the requested variables were found:
> cortex <- subset(cortex, image_imagerow > 275 & image_imagecol > 370, invert = TRUE)
Error in FetchData(object = object, vars = expr.char[vars.use], cells = cells, :
None of the requested variables were found:
> cortex <- subset(cortex, image_imagerow > 250 & image_imagecol > 440, invert = TRUE)
Error in FetchData(object = object, vars = expr.char[vars.use], cells = cells, :
None of the requested variables were found:
And I have try to use the solution: #1212 (comment) for subsetting on features that have a dash in their name. But it doesn't work.
So,I wonder the structure of seurat may be the key to solve the problem.
I tape:
cortex@images
and saw：
attr(,"class")
[1] "scalefactors"
Slot "coordinates":
tissue row col imagerow imagecol
AAACAATCTACTAGCA-1 1 3 43 1611 4170
AAACACCAATAACTGC-1 1 59 19 8315 2519
AAACAGAGCGACTCCT-1 1 14 94 2927 7679
I try change the imgine_imagerow into imagerow, and change the image_imagecol into the imagecol,but it doesn't work again.
And another question is : How can I further segment based on exact positions?
Because I don't know exactly about the coordinates of cortex.How the example in official website actually do in this step?
thanks!
下面有一個小哥給我的問題點了個贊，居然有些小開心。
作者的回答
Hi,
Please try replacing image_imagerow and image_imagecol with anterior1_imagerow and anterior1_imagecol.
This is still under active development but the do.identify parameter of SpatialDimPlot should allow you to select cells manually or at least give you a sense of where you could start to draw some cutoffs.
我的思考
- 感覺取子集這部分，有點像舊的空間轉錄組的流程的ST viewer這步生成坐標映射關系表的感覺
- 作者也說了，這個版本還在開發中，需要但是可以嘗試用下他的輸入參數
最近暫時還沒有空嘗試，不過出于Github的社交禮儀，還是想先對作者表示感謝~
