Hello, I used dior to convert to h5 and used diopy to integrate the two data. Then I used dior to read the integrated data and reported the following error. Do you know how to solve it? The two data contain 60w cells and 50w cells respectively.
library(dior)
obj1 <- readRDS("monkey1.rds")
obj2 <- readRDS("monkey2.rds")
obj1.sce <- as.SingleCellExperiment(obj1)
write_h5(obj1.sce, file='monkey1.h5', object.type = 'singlecellexperiment')
obj2.sce <- as.SingleCellExperiment(obj2)
write_h5(obj2.sce, file='monkey2.h5', object.type = 'singlecellexperiment')
import diopy
m1=diopy.input.read_h5(file = 'monkey1.h5')
m2 = diopy.input.read_h5(file = 'monkey2.h5')
var_names = m1.var_names.intersection(m2.var_names)
m1 = m1[:, var_names]
m2 = m2[:, var_names]
sc.pp.pca(m1)
sc.pp.neighbors(m1)
sc.tl.umap(m1)
sc.tl.ingest(m2, m1, obs='SubClass')
adata_concat = m1.concatenate(m2, batch_categories=['Monkey1', 'Monkey2'])
diopy.output.write_h5(adata_concat, file = 'monkey_merge.h5')
sc <- LoadH5Seurat("monkey_merge.h5seurat")
adata = dior::read_h5(file='monkey_merge.h5', target.object = 'singlecellexperiment', assay.name = "RNA")
<simpleError in if ((lp <- length(p)) < 1 || p[1] != 0 || any((dp <- p[-1] - p[-lp]) < 0)) stop("'p' must be a non-decreasing vector (0, ...)"): missing value where TRUE/FALSE needed>
Hello, I used dior to convert to h5 and used diopy to integrate the two data. Then I used dior to read the integrated data and reported the following error. Do you know how to solve it? The two data contain 60w cells and 50w cells respectively.
library(dior)
obj1 <- readRDS("monkey1.rds")
obj2 <- readRDS("monkey2.rds")
obj1.sce <- as.SingleCellExperiment(obj1)
write_h5(obj1.sce, file='monkey1.h5', object.type = 'singlecellexperiment')
obj2.sce <- as.SingleCellExperiment(obj2)
write_h5(obj2.sce, file='monkey2.h5', object.type = 'singlecellexperiment')
import diopy
m1=diopy.input.read_h5(file = 'monkey1.h5')
m2 = diopy.input.read_h5(file = 'monkey2.h5')
var_names = m1.var_names.intersection(m2.var_names)
m1 = m1[:, var_names]
m2 = m2[:, var_names]
sc.pp.pca(m1)
sc.pp.neighbors(m1)
sc.tl.umap(m1)
sc.tl.ingest(m2, m1, obs='SubClass')
adata_concat = m1.concatenate(m2, batch_categories=['Monkey1', 'Monkey2'])
diopy.output.write_h5(adata_concat, file = 'monkey_merge.h5')
sc <- LoadH5Seurat("monkey_merge.h5seurat")
adata = dior::read_h5(file='monkey_merge.h5', target.object = 'singlecellexperiment', assay.name = "RNA")
<simpleError in if ((lp <- length(p)) < 1 || p[1] != 0 || any((dp <- p[-1] - p[-lp]) < 0)) stop("'p' must be a non-decreasing vector (0, ...)"): missing value where TRUE/FALSE needed>