R语言拟时序报错如何解决

Question

问题遇到的现象和发生背景

根据视频学习单细胞测序拟时序分析中出现的报错应该怎么解决

问题相关代码，请勿粘贴截图

library(monocle)
data <- as(as.matrix(scRNA@assays$RNA@counts), 'sparseMatrix')

pd <- new('AnnotatedDataFrame', data = [e-mail])

fData <- data.frame(gene_short_name = row.names(data), row.names = row.names(data))
fd <- new('AnnotatedDataFrame', data = fData)

mycds <- newCellDataSet(data,
phenoData = pd,
featureData = fd,
expressionFamily = negbinomial.size())

save(mycds, file = "c:/Users/LWD/Desktop/scRNAseq/mycds_raw.Rdata")
rm(list = ls())
load("../../tmp/mycds_raw.Rdata")
#library("monocle")
mycds <- estimateSizeFactors(mycds)
mycds <- estimateDispersions(mycds, cores=4, relative_expr = TRUE) #!

load("../../tmp/markergene.Rdata")
markers.gene <- all.markers$gene
mycds <- setOrderingFilter(mycds, markers.gene)

mycds <- reduceDimension(mycds, max_components = 2, method = 'DDRTree') #!

mycds <- orderCells(mycds)
#save(mycds,file = "../../tmp/mycds_reduced.Rdata")
load("../../tmp/mycds_reduced.Rdata")

p1 <- plot_cell_trajectory(mycds, color_by = "seurat_clusters")
ggsave("../../out/3.4trajectory_1.pdf", plot = p1)
p2 <- plot_cell_trajectory(mycds, color_by = "State")
ggsave("../../out/3.4trajectory_2.pdf", plot = p2)

运行结果及报错内容

data <- as(as.matrix(scRNA@assays$RNA@counts), 'sparseMatrix')

pd <- new('AnnotatedDataFrame', data = [e-mail])
fData <- data.frame(gene_short_name = row.names(data), row.names = row.names(data))
fd <- new('AnnotatedDataFrame', data = fData)
mycds <- newCellDataSet(data,

•                     phenoData = pd,
  

•                     featureData = fd,
  

•                     expressionFamily = negbinomial.size())
  

  save(mycds, file = "c:/Users/LWD/Desktop/scRNAseq/mycds_raw.Rdata")
  mycds <- estimateSizeFactors(mycds)
  mycds <- estimateDispersions(mycds, cores=4, relative_expr = TRUE)
  Removing 95 outliers
  Warning messages:
  1: group_by_() was deprecated in dplyr 0.7.0.
  Please use group_by() instead.
  See vignette('programming') for more help
  This warning is displayed once every 8 hours.
  Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.
  2: select_() was deprecated in dplyr 0.7.0.
  Please use select() instead.
  This warning is displayed once every 8 hours.
  Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.
  markers.gene <- all.markers$gene
  mycds <- setOrderingFilter(mycds, markers.gene)
  mycds <- reduceDimension(mycds, max_components = 2, method = 'DDRTree')

p1 <- plot_cell_trajectory(mycds, color_by = "seurat_clusters")
mycds <- orderCells(mycds)
Error in if (class(projection) != "matrix") projection <- as.matrix(projection) :
the condition has length > 1
In addition: Warning message:
In graph.dfs(dp_mst, root = root_cell, neimode = "all", unreachable = FALSE, :
Argument neimode' is deprecated; use mode' instead

我的解答思路和尝试过的方法

感觉无从下手

我想要达到的结果

能解决报错并成功出图

Answer 1

您收到该错误是因为您只能评估 if (...) 中的单个 T/F。但是，data[1, ] < ... 是一个矢量化评估，它返回一个长度为 n 的 T/F 向量（即，对于上述情况，为 1000）。不过，我认为您的第二个函数 (est_L) 与该图像中显示的等式不匹配。