RRuntimeError: Error in validObject(.Object) :

[vincentxu199112]

in 3.5.1 Slingshot:
code section:
%%R -i adata_ent

#Plot 1
colour_map = brewer.pal(20,'Set1')
par(xpd=TRUE)
par(mar=c(4.5,5.5,2,7))
plot(reducedDims(adata_ent)$PCA[,1], reducedDims(adata_ent)$PCA[,2], col=colour_map[colData(adata_ent)$louvain_final], bty='L', xlab='PC1', ylab='PC2')
legend(x=12, y=12, legend=unique(colData(adata_ent)$louvain_final), fill=colour_map[as.integer(unique(colData(adata_ent)$louvain_final))])

print("1:")
adata_ent_start <- slingshot(adata_ent, clusterLabels = 'louvain_final', reducedDim = 'PCA', start.clus='Stem')
print(SlingshotDataSet(adata_ent_start))

print("")
print("2:")
adata_ent_startend <- slingshot(adata_ent, clusterLabels = 'louvain_final', reducedDim = 'PCA', start.clus='Stem', end.clus=c('Enterocyte mat. (Proximal)', 'Enterocyte mat. (Distal)'))
print(SlingshotDataSet(adata_ent_startend))

print("")
print("3:")
adata_ent_simple_startend <- slingshot(adata_ent, clusterLabels = 'louvain_r0.5', reducedDim = 'PCA', start.clus='Stem', end.clus='Enterocyte')
print(SlingshotDataSet(adata_ent_simple_startend))

error:
RRuntimeError: Error in validObject(.Object) :
invalid class "dgRMatrix" object: 1: invalid object for slot "p" in class "dgRMatrix": got class "array", should be or extend class "integer"
invalid class "dgRMatrix" object: 2: invalid object for slot "j" in class "dgRMatrix": got class "array", should be or extend class "integer"
invalid class "dgRMatrix" object: 3: invalid object for slot "Dim" in class "dgRMatrix": got class "array", should be or extend class "integer"
invalid class "dgRMatrix" object: 4: invalid object for slot "x" in class "dgRMatrix": got class "array", should be or extend class "numeric"

[LuckyMD]

Hi!

Could it be that you have rpy2 version > 3.4.2? Try downgrading rpy2 to 3.4.2. It looks like this issue: theislab/anndata2ri#63.