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wguo-research / scCancer

A package for automated processing of single cell RNA-seq data in cancer
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在运行cell interaction过程中，错误：没有getCellTypeColor这个函数 #18

Closed Yiquan-Jiang closed 4 years ago

Yiquan-Jiang commented 4 years ago

作者您好，在运行cell interaction过程中，出现错误：没有getCellTypeColor这个函数。我找了一下r语言里面getCellTypeColor，找不到哪个r包里面有这个函数？是不是函数更名了呢？

wguo-research commented 4 years ago

Could you please show me your codes and the error messages?

Yiquan-Jiang commented 4 years ago

Could you please show me your codes and the error messages?

t.results <- runSeurat(

  • expr = expr,
  • savePath = savePath,
  • pc.use = pc.use,
  • resolution = resolution,
  • clusterStashName = clusterStashName,
  • bool.runDiffExpr = bool.runDiffExpr
  • ) [2020-05-25 17:04:18] -----: PCA [2020-05-25 17:04:20] -----: clustering [2020-05-25 17:04:21] -----: tSNE [2020-05-25 17:04:33] -----: UMAP [2020-05-25 17:04:52] -----: differential expression analysis expr = t.results$expr cell.annotation = t.results$cell.annotation results[["diff.expr.genes"]] = t.results$diff.expr.genes rm(t.results) gc() results[["seurat.plots"]] <- plotSeurat(
  • expr = expr,
  • cell.annotation = cell.annotation,
  • show.features = show.features,
  • bool.add.features = bool.add.features,
  • coor.names = coor.names,
  • bool.runDiffExpr = bool.runDiffExpr,
  • diff.expr.genes = results[["diff.expr.genes"]],
  • n.markers = n.markers,
  • species = species,
  • savePath = savePath
  • ) [2020-05-25 17:15:30] -----: Seurat plotting and saving When using repel, set xnudge and ynudge to 0 for optimal results if(bool.runInteraction){
  • t.results <- runCellInteraction(expr, cellSetName = clusterStashName,
  • species = species, savePath = savePath)
  • results[["interaction.score"]] <- t.results$interaction.score

  • results[["inter.plot"]] <-

  • ggplot(t.results$stat.df, aes(x = Ligand.CellSet, y = Receptor.CellSet, size = Num, color = Sum)) +

  • geom_point() +

  • coord_fixed() +

  • scale_color_gradientn(colors = colorRampPalette(c("#FAFBFD", "#2e68b7"))(50)) +

  • theme_light() +

  • theme(axis.title.x = element_text(size = 13, vjust = -0.1),

  • axis.title.y = element_text(size = 13, vjust = 1.5),

  • axis.text.x = element_text(size = 11, angle = 45, hjust = 1),

  • axis.text.y = element_text(size = 11),

  • panel.border = element_rect(color = "black"))

  • results[["inter.plot"]] <- plotCellInteraction(t.results$stat.df, cell.annotation)
  • ggsave(filename = file.path(savePath, "figures/interaction-score.png"),
  • results[["inter.plot"]], width = 7, height = 6.5, dpi = 500)
  • } [2020-05-25 17:42:54] -----: cell interaction analysis

    **_Error in getCellTypeColor(cell.types = unique(cell.annotation[[sel.col]])) :

    没有"getCellTypeColor"这个函数_**

在运行完runseurat后，运行cell interaction analysis出现以上错误~

wguo-research commented 4 years ago

You can re-install and try it again.