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Source  : 633e320
Branch  : main
Author  : Andrew Ghazi <[email protected]>
Time    : 2024-09-08 16:51:30 +0000
Message : Merge pull request #26 from ccb-hms/add_exercises

Add exercises
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actions-user committed Sep 8, 2024
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236 changes: 14 additions & 222 deletions cell_type_annotation.md
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Expand Up @@ -730,238 +730,30 @@ overlaps in their marker sets. In the absence of prior annotation, a
more general diagnostic check is to compare the assigned labels to
cluster identities, under the expectation that most cells of a single
cluster would have the same label (or, if multiple labels are present,
they should at least represent closely related cell states).
they should at least represent closely related cell states). We only print out the top-left corner of the table here, but you should try looking at the whole thing:


``` r
new.labels <- colnames(results)[max.col(results)]

tab <- table(new.labels, sce$celltype.mapped)

tab
tab[1:4,1:4]
```

``` output
new.labels Allantois Blood progenitors 1
Allantois 28 0
Cardiomyocytes 0 0
Endothelium 0 0
Erythroid2 0 0
Erythroid3 0 0
ExE mesoderm 0 0
Forebrain/Midbrain/Hindbrain 1 0
Gut 0 0
Haematoendothelial progenitors 1 0
Intermediate mesoderm 0 0
Mesenchyme 0 0
Neural crest 11 4
NMP 0 0
Paraxial mesoderm 5 0
Pharyngeal mesoderm 0 0
Somitic mesoderm 0 0
Spinal cord 0 0
Surface ectoderm 0 0
new.labels Blood progenitors 2 Cardiomyocytes
Allantois 0 0
Cardiomyocytes 0 27
Endothelium 0 0
Erythroid2 1 0
Erythroid3 0 0
ExE mesoderm 0 0
Forebrain/Midbrain/Hindbrain 0 0
Gut 0 0
Haematoendothelial progenitors 0 0
Intermediate mesoderm 0 0
Mesenchyme 0 0
Neural crest 6 1
NMP 0 0
Paraxial mesoderm 0 4
Pharyngeal mesoderm 0 6
Somitic mesoderm 0 0
Spinal cord 0 0
Surface ectoderm 0 0
new.labels Caudal epiblast Caudal Mesoderm Def. endoderm
Allantois 0 0 0
Cardiomyocytes 0 0 0
Endothelium 0 0 0
Erythroid2 0 0 0
Erythroid3 0 0 0
ExE mesoderm 0 0 0
Forebrain/Midbrain/Hindbrain 1 0 2
Gut 0 0 0
Haematoendothelial progenitors 0 0 0
Intermediate mesoderm 0 0 0
Mesenchyme 0 0 0
Neural crest 0 0 1
NMP 0 0 0
Paraxial mesoderm 0 0 1
Pharyngeal mesoderm 0 0 0
Somitic mesoderm 0 1 1
Spinal cord 0 0 0
Surface ectoderm 0 0 0
new.labels Doublet Endothelium Erythroid1 Erythroid2
Allantois 0 0 0 0
Cardiomyocytes 0 0 0 0
Endothelium 0 13 0 0
Erythroid2 0 0 14 21
Erythroid3 0 0 6 5
ExE mesoderm 0 0 0 0
Forebrain/Midbrain/Hindbrain 6 0 0 0
Gut 0 0 0 0
Haematoendothelial progenitors 0 19 0 0
Intermediate mesoderm 13 0 0 0
Mesenchyme 0 0 0 0
Neural crest 20 1 3 0
NMP 0 0 0 0
Paraxial mesoderm 5 0 0 0
Pharyngeal mesoderm 1 0 0 0
Somitic mesoderm 1 0 0 0
Spinal cord 1 0 0 0
Surface ectoderm 0 0 0 0
new.labels Erythroid3 ExE mesoderm
Allantois 0 0
Cardiomyocytes 0 0
Endothelium 0 0
Erythroid2 51 0
Erythroid3 49 0
ExE mesoderm 0 23
Forebrain/Midbrain/Hindbrain 0 1
Gut 0 0
Haematoendothelial progenitors 0 0
Intermediate mesoderm 0 16
Mesenchyme 0 0
Neural crest 0 17
NMP 0 0
Paraxial mesoderm 0 0
Pharyngeal mesoderm 0 0
Somitic mesoderm 0 0
Spinal cord 0 0
Surface ectoderm 0 0
new.labels Forebrain/Midbrain/Hindbrain Gut
Allantois 0 0
Cardiomyocytes 0 0
Endothelium 0 0
Erythroid2 0 0
Erythroid3 0 0
ExE mesoderm 0 0
Forebrain/Midbrain/Hindbrain 83 4
Gut 0 5
Haematoendothelial progenitors 0 0
Intermediate mesoderm 0 0
Mesenchyme 0 0
Neural crest 20 0
NMP 0 0
Paraxial mesoderm 0 0
Pharyngeal mesoderm 0 0
Somitic mesoderm 0 0
Spinal cord 0 0
Surface ectoderm 0 12
new.labels Haematoendothelial progenitors
Allantois 0
Cardiomyocytes 0
Endothelium 0
Erythroid2 0
Erythroid3 0
ExE mesoderm 0
Forebrain/Midbrain/Hindbrain 0
Gut 0
Haematoendothelial progenitors 16
Intermediate mesoderm 0
Mesenchyme 0
Neural crest 8
NMP 0
Paraxial mesoderm 2
Pharyngeal mesoderm 0
Somitic mesoderm 0
Spinal cord 0
Surface ectoderm 0
new.labels Intermediate mesoderm Mesenchyme Neural crest
Allantois 0 0 0
Cardiomyocytes 0 0 0
Endothelium 0 0 0
Erythroid2 0 0 0
Erythroid3 0 0 0
ExE mesoderm 1 7 0
Forebrain/Midbrain/Hindbrain 0 3 0
Gut 0 0 0
Haematoendothelial progenitors 0 0 0
Intermediate mesoderm 9 15 0
Mesenchyme 0 69 0
Neural crest 4 4 10
NMP 0 0 0
Paraxial mesoderm 0 7 0
Pharyngeal mesoderm 0 13 0
Somitic mesoderm 2 0 0
Spinal cord 0 0 0
Surface ectoderm 0 0 0
new.labels NMP Paraxial mesoderm Pharyngeal mesoderm
Allantois 0 0 0
Cardiomyocytes 0 0 0
Endothelium 0 0 0
Erythroid2 0 0 0
Erythroid3 0 0 0
ExE mesoderm 0 0 0
Forebrain/Midbrain/Hindbrain 41 2 4
Gut 0 0 0
Haematoendothelial progenitors 0 0 0
Intermediate mesoderm 0 1 5
Mesenchyme 0 0 0
Neural crest 5 20 10
NMP 16 0 0
Paraxial mesoderm 0 43 3
Pharyngeal mesoderm 0 0 18
Somitic mesoderm 0 0 0
Spinal cord 0 0 0
Surface ectoderm 0 0 0
new.labels Rostral neurectoderm Somitic mesoderm
Allantois 0 0
Cardiomyocytes 0 0
Endothelium 0 0
Erythroid2 0 0
Erythroid3 0 0
ExE mesoderm 0 0
Forebrain/Midbrain/Hindbrain 11 1
Gut 0 0
Haematoendothelial progenitors 0 0
Intermediate mesoderm 0 2
Mesenchyme 0 0
Neural crest 0 7
NMP 0 0
Paraxial mesoderm 0 0
Pharyngeal mesoderm 0 0
Somitic mesoderm 0 25
Spinal cord 0 0
Surface ectoderm 0 0
new.labels Spinal cord Stripped Surface ectoderm
Allantois 0 0 0
Cardiomyocytes 0 0 0
Endothelium 0 1 0
Erythroid2 0 1 0
Erythroid3 0 1 0
ExE mesoderm 0 0 0
Forebrain/Midbrain/Hindbrain 37 0 17
Gut 0 0 2
Haematoendothelial progenitors 0 0 0
Intermediate mesoderm 0 0 0
Mesenchyme 0 0 2
Neural crest 3 5 6
NMP 0 0 0
Paraxial mesoderm 0 0 0
Pharyngeal mesoderm 0 0 0
Somitic mesoderm 0 0 0
Spinal cord 9 0 0
Surface ectoderm 0 0 20
new.labels Allantois Blood progenitors 1 Blood progenitors 2
Allantois 28 0 0
Cardiomyocytes 0 0 0
Endothelium 0 0 0
Erythroid2 0 0 1
new.labels Cardiomyocytes
Allantois 0
Cardiomyocytes 27
Endothelium 0
Erythroid2 0
```

As a diagnostic measure, we examine the distribution of AUCs across
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4 changes: 2 additions & 2 deletions md5sum.txt
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Expand Up @@ -6,8 +6,8 @@
"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-09-06"
"episodes/intro-sce.Rmd" "538e5f4aa0dde4a6cb09a342d8dc867d" "site/built/intro-sce.md" "2024-09-06"
"episodes/eda_qc.Rmd" "1e88f395d30778f4526532deea43eb03" "site/built/eda_qc.md" "2024-09-06"
"episodes/cell_type_annotation.Rmd" "a586bd88d56159adebaf315580fa2285" "site/built/cell_type_annotation.md" "2024-09-08"
"episodes/multi-sample.Rmd" "e33ec8bf5cfd26471d17fce4d6af9281" "site/built/multi-sample.md" "2024-09-06"
"episodes/cell_type_annotation.Rmd" "66af56b730aaa88e937bc1743afb471a" "site/built/cell_type_annotation.md" "2024-09-08"
"episodes/multi-sample.Rmd" "2d38d9903358ea8a8067abd82a1f1f54" "site/built/multi-sample.md" "2024-09-08"
"episodes/large_data.Rmd" "bbe443f474a0823122658effa2beb57e" "site/built/large_data.md" "2024-09-06"
"episodes/hca.Rmd" "6db220495ae4ae56d33e4ca5b5f9b8ae" "site/built/hca.md" "2024-09-06"
"instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-09-06"
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