Blending gene expression in SpatialFeaturePlot

[AnjaK88]

Hi Team,

this issue came up in #6095 already. I wanted to ask whether you are planning to include the "blend" option (if possible at all) in the SpatialFeaturePlot? As the ImageFeaturePlot function does not seem to be compatible with 10x Visium data.

Cheers

[george-hall-ucl]

Hi, I have now written a function to do this, see here: https://github.com/satijalab/seurat/issues/6095#issuecomment-1973063131.

Thanks, George

[dfeng4127]

Hi, I have now written a function to do this, see here: #6095 (comment).

Thanks, George

hi, i use it to plot my ST data, but find error :

SpatialFeaturePlotBlend(object = ST2, features = c("HSPB1",'CD79A')) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'nrow': no slot of name "coordinates" for this object of class "VisiumV2" Called from: h(simpleError(msg, call)) Browse[1]>

can you fix it?

[george-hall-ucl]

Hi, I have now written a function to do this, see here: #6095 (comment). Thanks, George

hi, i use it to plot my ST data, but find error :

SpatialFeaturePlotBlend(object = ST2, features = c("HSPB1",'CD79A')) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'nrow': no slot of name "coordinates" for this object of class "VisiumV2" Called from: h(simpleError(msg, call)) Browse[1]>

can you fix it?

Hi,

It looks like the image slot "VisiumV2" does not have an associated coordinates slot. Do you have multiple images present, and if so, is this one that you want to plot? If you are able to plot it using SpatialDimPlot, then I guess it must have some form of coordinates? It might just be a case of renaming that slot to "coordinates", which is what SpatialDimPlotBlend expects.

P.S. now that there is a repository for this function, please submit any issues on there.

Thanks, George

[dfeng4127]

Ok,thanks , maybe the the Seurat version problem , I have got the same error

发件人: George Hall @.> 日期: 星期一, 2024年7月15日 16:12 收件人: satijalab/seurat @.> 抄送: dfeng4127 @.>, Comment @.> 主题: Re: [satijalab/seurat] Blending gene expression in SpatialFeaturePlot (Issue #7553)

Hi, I have now written a function to do this, see here: #6095 (comment)https://github.com/satijalab/seurat/issues/6095#issuecomment-1973063131. Thanks, George

hi, i use it to plot my ST data, but find error :

SpatialFeaturePlotBlend(object = ST2, features = c("HSPB1",'CD79A')) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'nrow': no slot of name "coordinates" for this object of class "VisiumV2" Called from: h(simpleError(msg, call)) Browse[1]>

can you fix it?

Hi,

It looks like the image slot "VisiumV2" does not have an associated coordinates slot. Do you have multiple images present, and if so, is this one that you want to plot? If you are able to plot it using SpatialDimPlot, then I guess it must have some form of coordinates? It might just be a case of renaming that slot to "coordinates", which is what SpatialDimPlotBlend expects.

Thanks, George

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