Is any code grammer wrong？

[Hui-XiangZhang]

Describe the bug

library("cellxgene.census") census <- open_soma() library("Seurat")

I want to search the Gene Expressions of ACTB

seurat_obj <- get_seurat( census, "Homo sapiens", obs_column_names = c("cell_type", "disease"), var_value_filter = "feature_id %in% c('ENSG00000075624')", obs_value_filter = "disease == 'lung carcinoma'" ) seurat_obj

Error: 'cells' must have a length of 0

Is any code grammer wrong？

Environment

MacOS 12.7 R: Seurat V4.4

[ebezzi]

Hey @Hui-XiangZhang ,

the query is returning no values because 'lung carcinoma' is too generic as a value for disease. You can see what values are valid for disease by running this snippet:

table <- census$get("census_data")$get("homo_sapiens")$obs$read(
  column_names = c("disease"),
)$concat()

df <- as.data.frame(table)

unique(df$disease)

Let me know if you have any further questions.

[Hui-XiangZhang]

Hey @Hui-XiangZhang ,

the query is returning no values because 'lung carcinoma' is too generic as a value for disease. You can see what values are valid for disease by running this snippet:

table <- census$get("census_data")$get("homo_sapiens")$obs$read(
  column_names = c("disease"),
)$concat()

df <- as.data.frame(table)

unique(df$disease)

Let me know if you have any further questions.

Thanks, it works when I change "disease == 'lung carcinoma'" to "obs_value_filter = "disease == 'lung adenocarcinoma'"". A really good project! Hope more and more scRNAseq data will be uploaded and provide fastqs. Have a nice day.

[Hui-XiangZhang]

Hey @Hui-XiangZhang ,

the query is returning no values because 'lung carcinoma' is too generic as a value for disease. You can see what values are valid for disease by running this snippet:

table <- census$get("census_data")$get("homo_sapiens")$obs$read(
  column_names = c("disease"),
)$concat()

df <- as.data.frame(table)

unique(df$disease)

Let me know if you have any further questions.

unique(df$disease) [1] "normal" "B-cell acute lymphoblastic leukemia"
[3] "Lewy body dementia" "Parkinson disease"
[5] "periodontitis" "gingivitis"
[7] "epilepsy" "digestive system disorder"
[9] "dementia" "nonpapillary renal cell carcinoma"
[11] "kidney oncocytoma" "kidney benign neoplasm"
[13] "clear cell renal carcinoma" "B-cell non-Hodgkin lymphoma"
[15] "breast cancer" "pulmonary fibrosis"
[17] "squamous cell lung carcinoma" "COVID-19"
[19] "lung adenocarcinoma" "chronic obstructive pulmonary disease"
[21] "pulmonary sarcoidosis" "pneumonia"
[23] "lymphangioleiomyomatosis" "interstitial lung disease"
[25] "cystic fibrosis" "chronic rhinitis"
[27] "pleomorphic carcinoma" "lung large cell carcinoma"
[29] "hypersensitivity pneumonitis" "non-specific interstitial pneumonia"
[31] "chromophobe renal cell carcinoma" "plasma cell myeloma"
[33] "Crohn disease" "pilocytic astrocytoma"
[35] "type 2 diabetes mellitus" "gastritis"
[37] "Barrett esophagus" "gastric intestinal metaplasia"
[39] "gastric cancer" "common variable immunodeficiency"
[41] "pulmonary emphysema" "Down syndrome"
[43] "cataract" "basal laminar drusen"
[45] "age related macular degeneration 7" "adenocarcinoma"
[47] "neuroendocrine carcinoma" "non-small cell lung carcinoma"
[49] "glioblastoma" "acute myeloid leukemia"
[51] "acute promyelocytic leukemia" "myocardial infarction"
[53] "dilated cardiomyopathy" "arrhythmogenic right ventricular cardiomyopathy" [55] "non-compaction cardiomyopathy" "blastoma"
[57] "small cell lung carcinoma" "Crohn ileitis"
[59] "post-COVID-19 disorder" "Wilms tumor"
[61] "follicular lymphoma" "influenza"
[63] "acute kidney failure" "chronic kidney disease"
[65] "hydrosalpinx" "respiratory system disorder"
[67] "systemic lupus erythematosus" "benign prostatic hyperplasia"
[69] "Alzheimer disease" "temporal lobe epilepsy"
[71] "trisomy 18" "type 1 diabetes mellitus"