anders-biostat / single-cell-lymphoma-explorer

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Cluster identities for all cells? #1

Open jeremymsimon opened 2 months ago

jeremymsimon commented 2 months ago

It seems the B cell cluster identities provided in metaInfo.rds represent a subset of cells (n=6000 of 26594 total). Is there a way to provide the cluster annotations for all T and B cells, ie the ones shown in the UMAP here and Fig 2-3 in the paper? I can't find this information for all cells in the paper or its associated materials or links

Thanks!

# Retrieved from this repository
meta <- readRDS("metaInfo.rds")
dim(meta$tcells)
[1] 8862    3

head(meta$tcells)
                           UMAP1      UMAP2 Subset
tFL2_AAACGGGTCTTGACGA  -8.533787  1.8456780      0
tFL2_AAAGCAAAGGCGCTCT -10.233397  0.1493033      0
tFL2_AAATGCCGTAGCACGA -11.285441  0.3282457      0
tFL2_AACCATGGTACCAGTT  -9.991895  0.8565457      0
tFL2_AAGTCTGAGATGGCGT -10.947859 -0.2834946      0
tFL2_AAGTCTGTCCGCGCAA  -6.584951  2.0932305      3

dim(meta$bcells)
[1] 6000    3

head(meta$bcells)
                          UMAP1     UMAP2 Subset
tFL2_GATTCAGAGCTGGAAC -3.726201 -7.181145      5
tFL2_AACACGTCACACAGAG -3.260301 -5.485855      5
tFL2_ACATCAGGTTCCGGCA -4.213102 -6.762125      5
tFL2_CCCAGTTTCACCGGGT -3.345386 -5.145964      5
tFL2_ACTTGTTTCGTGGACC -4.179855 -6.458187      5
tFL2_CTCGTCATCACCGGGT -2.707596 -6.752877      5

# Retrieved from https://heidata.uni-heidelberg.de/dataset.xhtml?persistentId=doi:10.11588/data/VRJUNV
annot_b <- read_delim("AnnotationBcells.csv",delim=";")
dim(annot_b)
[1] 26594     3

annot_b %>% 
   group_by(Population) %>% 
   summarize(n = n())

# A tibble: 3 × 2
  Population     n
  <chr>      <int>
1 HealthyB    3691
2 MalignantB 22673
3 Myeloid      230

annot_t <- read_delim("Annotation_Tcells.csv",delim=";")   
dim(annot_t)
[1] 8862    3

annot_t %>% 
   group_by(Population) %>% 
   summarize(n = n())

# A tibble: 4 × 2
  Population     n
  <chr>      <int>
1 TFH         1683
2 TH          3488
3 TREG         917
4 TTOX        2774
jeremymsimon commented 1 month ago

@simon-anders @DietrichLab any way to share these metadata?