舊號(hào)無故被封蓝晒，小號(hào)再發(fā)一次

更多空間轉(zhuǎn)錄組文章：

1. 新版10X Visium

• 【10X空間轉(zhuǎn)錄組Visium】（一）Space Ranger 1.0.0(更新于20191205）
• 【10X空間轉(zhuǎn)錄組Visium】（二）Loupe Browser 4.0.0
• 【10X空間轉(zhuǎn)錄組Visium】（三）跑通Visium全流程記錄
• 【10X空間轉(zhuǎn)錄組Visium】（四）R下游分析的探索性代碼示例
  
• 【10X空間轉(zhuǎn)錄組Visium】（五）Visium原理咙咽、流程與產(chǎn)品
• 【10X空間轉(zhuǎn)錄組Visium】（六）新版Seurat v3.2分析Visium空間轉(zhuǎn)錄組結(jié)果的代碼實(shí)操
• 【10X空間轉(zhuǎn)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(zhuǎn)錄組Spatial】（一）ST Spot Detector使用指南
• 【舊版空間轉(zhuǎn)錄組Spatial】（二）跑通流程試驗(yàn)記錄
• 【舊版空間轉(zhuǎn)錄組Spatial】（三）ST Spot Detector實(shí)操記錄

問題描述：

在對自己跑出來的空間轉(zhuǎn)錄組數(shù)據(jù)用Seurat V3.2進(jìn)行分析時(shí)取子集遇到一個(gè)問題凄杯，我不知道該如何選取像素點(diǎn)坐標(biāo)梗夸，以及用官網(wǎng)給的字段會(huì)出現(xiàn)報(bào)錯(cuò)的情況，于是我在Github上作者大神提問，不出意外歹垫，下面也有一個(gè)跟我遇到的情況類似的娶耍。

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(gè)小哥給我的問題點(diǎn)了個(gè)贊，居然有些小開心擦耀。

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

• 感覺取子集這部分棉圈，有點(diǎn)像舊的空間轉(zhuǎn)錄組的流程的ST viewer這步生成坐標(biāo)映射關(guān)系表的感覺
• 作者也說了，這個(gè)版本還在開發(fā)中眷蜓，需要但是可以嘗試用下他的輸入?yún)?shù)

最近暫時(shí)還沒有空嘗試分瘾，不過出于Github的社交禮儀，還是想先對作者表示感謝~