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Single-cell spatial + Gene Expression

Source: R/seqFISH.R
seqFISH.Rd

seqFISH function assembles data on-the-fly from ExperimentHub to provide a MultiAssayExperiment container. Actually the DataType argument provides access to the available datasets associated to the package.

Usage

seqFISH(
  DataType = "mouse_visual_cortex",
  modes = "*",
  version,
  dry.run = TRUE,
  verbose = TRUE,
  ...
)

Arguments

DataType

character(1) indicating the identifier of the dataset to retrieve. (default "mouse_visual_cortex")

modes

character() The assay types or modes of data to obtain these include seq-FISH and scRNA-seq data by default.

version

character(1) Either version '1.0.0' or '2.0.0' depending on data version required (default '1.0.0'). See version section.

dry.run

logical(1) Whether to return the dataset names before actual download (default TRUE)

verbose

logical(1) Whether to show the dataset currently being (down)loaded (default TRUE)

...

Additional arguments passed on to the ExperimentHub-class constructor

Value

A MultiAssayExperiment of seq-FISH data

Details

seq FISH data are a combination of single cell spatial coordinates and transcriptomics for a few hundreds of genes. seq-FISH data can be combined for example with scRNA-seq data to unveil multiple aspects of cellular behaviour based on their spatial organization and transcription.

Available datasets are:

  • mouse_visual_cortex: combination of seq-FISH data as obtained from Zhu et al. (2018) and scRNA-seq data as obtained from Tasic et al. (2016), Version 1.0.0 returns the full scRNA-seq data matrix, while version 2.0.0 returns the processed and subsetted scRNA-seq data matrix (produced for the Mathematical Frameworks for Integrative Analysis of Emerging Biological Data Types 2020 Workshop) The returned seqFISH data are always the processed ones for the same workshop. Additionally, cell types annotations are available in the colData through the class column in the seqFISH assay.

    • scRNA_Counts - Tasic scRNA-seq gene count matrix

    • scRNA_Labels - Tasic scRNA-seq cell labels

    • seqFISH_Coordinates - Zhu seq-FISH spatial coordinates

    • seqFISH_Counts - Zhu seq-FISH gene counts matrix

    • seqFISH_Labels - Zhu seq-FISH cell labels

Author

Dario Righelli <dario.righelli gmail.com>

Examples


seqFISH(DataType = "mouse_visual_cortex", modes = "*", version = "2.0.0",
    dry.run = TRUE)
#>    ah_id                mode file_size rdataclass rdatadateadded
#> 1 EH3785        scRNA_Counts    0.2 Mb     matrix     2020-09-14
#> 2 EH3786        scRNA_Labels      0 Mb data.frame     2020-09-14
#> 3 EH3787 seqFISH_Coordinates      0 Mb data.frame     2020-09-14
#> 4 EH3788      seqFISH_Counts    0.2 Mb     matrix     2020-09-14
#> 5 EH3789      seqFISH_Labels      0 Mb data.frame     2020-09-14
#>   rdatadateremoved
#> 1             <NA>
#> 2             <NA>
#> 3             <NA>
#> 4             <NA>
#> 5             <NA>