library(monocle)
library(HSMMSingleCell)
context("plotCellTrajectory")
data(HSMM_expr_matrix)
data(HSMM_gene_annotation)
data(HSMM_sample_sheet)
pd <- new("AnnotatedDataFrame", data = HSMM_sample_sheet)
fd <- new("AnnotatedDataFrame", data = HSMM_gene_annotation)
HSMM <- newCellDataSet(as.matrix(HSMM_expr_matrix),
phenoData = pd,
featureData = fd)
rpc_matrix <- relative2abs(HSMM)
HSMM <- newCellDataSet(as(as.matrix(rpc_matrix), "sparseMatrix"),
phenoData = pd,
featureData = fd,
lowerDetectionLimit=1,
expressionFamily=negbinomial.size())
test_that("plot_cell_trajectory() throws an error if reduceDimensionality hasn't been called yet", {
expect_error(plot_cell_trajectory(HSMM))
})
test_that("plot_cell_trajectory() throws an error if the CellDataSet's reduction method is unrecognizable", {
HSMM <- estimateSizeFactors(HSMM)
HSMM <- estimateDispersions(HSMM)
HSMM@dim_reduce_type <- "asdasd"
expect_error(plot_cell_trajectory(HSMM), "Error: unrecognized dimensionality reduction method.")
})
pd <- new("AnnotatedDataFrame", data = HSMM_sample_sheet)
fd <- new("AnnotatedDataFrame", data = HSMM_gene_annotation)
HSMM <- newCellDataSet(as.matrix(HSMM_expr_matrix),
phenoData = pd,
featureData = fd)
rpc_matrix <- relative2abs(HSMM)
HSMM <- newCellDataSet(as(as.matrix(rpc_matrix), "sparseMatrix"),
phenoData = pd,
featureData = fd,
lowerDetectionLimit=1,
expressionFamily=negbinomial.size())
#test_that("plot_cell_trajectory() is able to scale markers linearly and logarithmically", {
# HSMM <- estimateSizeFactors(HSMM)
# HSMM <- estimateDispersions(HSMM)
# HSMM <- clusterCells(HSMM, num_clusters=2)
# expect_error(plot_cell_trajectory(HSMM, markers = "MYH3"), NA)
# expect_error(plot_cell_trajectory(HSMM, markers = "MYH3", markers_linear = TRUE), NA)
#})
#test_that("plot_cell_trajectory() is able to run without the presence of markers", {
# HSMM <- estimateSizeFactors(HSMM)
# HSMM <- estimateDispersions(HSMM)
# HSMM <- clusterCells(HSMM, num_clusters=2)
# expect_error(plot_cell_trajectory(HSMM), NA)
#})
#test_that("plot_cell_trajectory() is able to show cell names", {
# HSMM <- estimateSizeFactors(HSMM)
# HSMM <- estimateDispersions(HSMM)
# HSMM <- clusterCells(HSMM, num_clusters=2)
# expect_error(plot_cell_trajectory(HSMM, show_cell_names = TRUE), NA)
#})
#test_that("plot_cell_trajectory() is able to show cell state numbers", {
# HSMM <- estimateSizeFactors(HSMM)
# HSMM <- estimateDispersions(HSMM)
# HSMM <- clusterCells(HSMM, num_clusters=2)
# expect_error(plot_cell_trajectory(HSMM, show_state_number = TRUE), NA)
#})
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