Help on R code to identify specific cells expressing lefty1 or lefty2

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@mmccoy @LindsayHayes @cpozmanter
Last semester I analyzed the gene expression of Lefty1 and Lefty2. I focused on the differential expression of each within celltypes and found that they were both expressed in the definitive endoderm and nascent mesoderm at one point during gastrulation. From there I wanted to focus on whether they were both expressed within the same cells, rather than the same celltypes. I left off with this graph…

Screen Shot 2022-06-16 at 2.28.33 PM
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Screen Shot 2022-06-16 at 2.32.28 PM
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The dots on the y-axis are cells that only have Lefty2 and the dots on the X-axis are cells that only hold Lefty1. Everything in between are cells that have different expression levels of either gene. I’m now interested in finding a code that identifies these cells.
I have a copy of my R notebook under the c_moor_ccc_su22_public folder.

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It’s great that you still want to keep working on this! You can filter the cells that express both Lefty1 and Lefty2. Here is one way to identify the cells:

data.df <- tibble(
    cell = sce$cell,
    geneA = logcounts(sce)[gene_A,], 
    geneB = logcounts(sce)[gene_B,]) %>% 
  filter(
    geneA > 0,
    geneB > 0)
coi <- colData(sce)$cell[colData(sce)$cell %in% data.df$cell]
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