Contents

1 Road map

2 A paper on the atlas of the prostate

overview

overview

normals

normals

2.1 The hca package

2.1.1 Surveying projects of the HCA

## 0/0 packages newly attached/loaded, see sessionInfo() for details.
## 0/0 packages newly attached/loaded, see sessionInfo() for details.

2.1.2 Picking a project; Enumerating and downloading loom files

## [1] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"

2.1.3 Working with loom

Very superficial filtering (to 60000 cells) and development of PCA

Whatchaget:

## $last_modified
## [1] "20210616T032315.280827Z"
## 
## $CreationDate
## [1] "20210616T030548.106180Z"
## 
## $LOOM_SPEC_VERSION
## [1] "3.0.0"
## 
## $expression_data_type
## [1] "exonic"
## 
## $input_id
## [1] "5012cf4f-ba5c-4928-aea1-ab2891e34323"
## 
## $input_id_metadata_field
## [1] "sequencing_process.provenance.document_id"
## 
## $input_name
## [1] "D27PrTzF_Edn"
## 
## $input_name_metadata_field
## [1] "sequencing_input.biomaterial_core.biomaterial_id"
## 
## $optimus_output_schema_version
## [1] "1.0.0"
## 
## $pipeline_version
## [1] "Optimus_v4.2.3"
> str(litsf2) # 22MB on disk (no quantifications)
Formal class 'DelayedMatrix' [package "DelayedArray"] with 1 slot
  ..@ seed:Formal class 'DelayedAperm' [package "DelayedArray"] with 2 slots
  .. .. ..@ perm: int [1:2] 2 1
  .. .. ..@ seed:Formal class 'DelayedSubset' [package "DelayedArray"] with 2 slots
  .. .. .. .. ..@ index:List of 2
  .. .. .. .. .. ..$ : int [1:60000] 1 2 3 4 5 6 7 8 9 10 ...
  .. .. .. .. .. ..$ : int [1:23420] 13 20 22 23 31 33 34 35 36 37 ...
  .. .. .. .. ..@ seed :Formal class 'HDF5ArraySeed' [package "HDF5Array"] with 7 slots
  .. .. .. .. .. .. ..@ filepath : chr "/home/stvjc/.cache/R/hca/36e582f7c6e_36e582f7c6e.loom"
  .. .. .. .. .. .. ..@ name     : chr "/matrix"
  .. .. .. .. .. .. ..@ as_sparse: logi FALSE
  .. .. .. .. .. .. ..@ type     : chr NA
  .. .. .. .. .. .. ..@ dim      : int [1:2] 382197 58347
  .. .. .. .. .. .. ..@ chunkdim : int [1:2] 64 64
  .. .. .. .. .. .. ..@ first_val: int 0
stvjc@stvjc-XPS-13-9300:~/CSAMA_HCA$ ls -tl /home/stvjc/.cache/R/hca/36e582f7c6e_36e582f7c6e.loom
-rw-rw-r-- 1 stvjc stvjc 1206062245 Jun 21 22:37 /home/stvjc/.cache/R/hca/36e582f7c6e_36e582f7c6e.loom

2.1.4 Working with iSEE

  • Question: where is the “stop/exit” button?
  • Question: can we embed iSEE (or components) in a vignette? Or is there an iSEE server?
context

context

fgf2

fgf2

2.2 Upshots

  • easy to survey HCA with hca package
  • easy to get experiments, metadata, quantifications for projects of interest
  • iSEE really accelerates exploration and elaboration of data and claims

3 Ontologies, EBI OLS, rols (thanks Laurent Gatto!), ontoProc::ctmarks

3.1 rols: Basic idea

  • OLS is ontology lookup service
  • has API
  • rols package help to interrogate the service
  • ontologies are everywhere

3.2 Learn about ‘smooth muscle’ with rols

## 0/0 packages newly attached/loaded, see sessionInfo() for details.
## Object of class 'OlsSearch':
##   query: smooth muscle 
##   requested: 100 (out of 47980)
##   response(s): 0

3.3 ontoProc – capitalizing on ontologyIndex (thanks Daniel Greene!), Rgraphviz (thanks Kasper Hansen!)

Innovation here: walk through linked ontologies such as PR and present additional facets about the concept in focus

Limitation: the OBO representation in use is outdated and out-links are sparse

library(ontoProc)
cl = getCellOnto()
chk = ctmarks(cl)

Projects: - use rols to get more interesting information about terms into the app - update the ontology resources - go beyond OBO … but not all the way to OWL? Evaluate the UI/UX needed to broaden ontology usage - impacts: data integration, precision of annotation, cognitive efficiency

4 shinywow2 - check out vjcitn.shinyapps.io/tnt4dn8 but be patient and don’t do it while i am doing it …