Different result in motif deviation score #2105
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zhenglab2023
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When I tried to plot the density distribution of motif deviation score by myself, I exacted the score as following.
score <- getMatrixFromProject(ArchRProj = proj, useMatrix = "MotifMatrix")
score <- score@assays@data$z
plot_data <- data.frame(score['DNMT1_301', ])
colnames(plot_data) <- "dev_score"
plot_data <- plot_data[rownames(proj@cellColData), ]
plot_data$CellType <- proj@cellColData$CellType
ggplot(plot_data, aes(x = dev_score, y = 'ident')) + geom_density_ridges_gradient() + facet_grid(CellType ~ ., scales = "free_y")
But I found that the generated output is different from the result generated from the following code.
p <- plotGroups(ArchRProj = proj, groupBy = "CellType", colorBy = "MotifMatrix", name = markerMotifs, imputeWeights = getImputeWeights(proj_bulk) )
Would you tell me the reasons in this problem? Thank you!
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