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hemberg-lab / scmap

A tool for unsupervised projection of single cell RNA-seq data
http://bioconductor.org/packages/scmap
GNU General Public License v3.0
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large part of the heatmap of select features is blank #17

Open Jiam1ng opened 5 years ago

Jiam1ng commented 5 years ago

when I draw heatmap after index cluster, it turned out a big blank, is this normal to see? here is my code: proj.sce <- SingleCellExperiment(assays = list(normcounts = proj.mat), colData = proj.cellname) logcounts(proj.sce) <- log2(normcounts(proj.sce)+1) rowData(proj.sce)$feature_symbol <- rownames(proj.sce) proj.sce <- selectFeatures(proj.sce, suppress_plot=F) proj.sce <- indexCluster(proj.sce) heatmap(as.matrix(metadata(proj.sce)$scmap_cluster_index))

Jiam1ng commented 5 years ago

and even when I project my dataset to itself, the the similarity is low and labels are all 'unassigned', is there any mistake I have made? thank you

Jiam1ng commented 5 years ago

I set the n_feature very few till there is no blank, but still when I project the dataset to itself, most of the cells are 'unassigned'

wikiselev commented 5 years ago

how does your proj.mat look like? what is the output of proj.mat[1:10,1:10]

Jiam1ng commented 5 years ago

@wikiselev thanks for your reply, here is the output: f1_GCGTCGGAGTTT f1_GCGCACCATCAA f1_AAGTGGTGTTGT f1_ACTTCTCTTAAN 0610005C13RIK 0 0 0 0 0610006L08RIK 0 0 0 0 0610009B22RIK 0 0 0 0 0610009E02RIK 0 0 1 0 0610009L18RIK 0 0 0 0 0610009O20RIK 0 0 0 2 0610010F05RIK 0 1 2 1 0610012G03RIK 0 0 0 0 0610025J13RIK 0 0 0 0 0610030E20RIK 0 0 0 0 f1_TGGTTCCTTTGC f1_CTCGACGCTCCN f1_CAGGTCCAGCCA f1_ACAGTCTATGGC 0610005C13RIK 0 0 0 0 0610006L08RIK 0 0 0 0 0610009B22RIK 0 0 0 0 0610009E02RIK 0 0 0 0 0610009L18RIK 0 0 0 0 0610009O20RIK 0 0 0 0 0610010F05RIK 4 2 1 1 0610012G03RIK 0 0 0 0 0610025J13RIK 0 0 0 0 0610030E20RIK 1 0 1 0 f1_TTAACCGCAATN f1_CGACAACTTCCC 0610005C13RIK 0 0 0610006L08RIK 0 0 0610009B22RIK 0 0 0610009E02RIK 0 0 0610009L18RIK 0 0 0610009O20RIK 0 0 0610010F05RIK 1 0 0610012G03RIK 0 0 0610025J13RIK 0 0 0610030E20RIK 0 0

wikiselev commented 5 years ago

thanks, looks good to me. Hard to think why this happens without looking at your data, though...

huiyuz commented 4 years ago

I have the same issue. I have no idea what happened. It seems associated with the selected feature genes. If I use the top 500 features, I got a small blank region, but if I use the top 1000 features, I got a huge gap of blank.