Package: tidySpatialExperiment 1.3.0

William Hutchison

tidySpatialExperiment: SpatialExperiment with tidy principles

tidySpatialExperiment provides a bridge between the SpatialExperiment package and the tidyverse ecosystem. It creates an invisible layer that allows you to interact with a SpatialExperiment object as if it were a tibble; enabling the use of functions from dplyr, tidyr, ggplot2 and plotly. But, underneath, your data remains a SpatialExperiment object.

Authors:William Hutchison [aut, cre], Stefano Mangiola [aut]

# Install 'tidySpatialExperiment' in R:

install.packages('tidySpatialExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/william-hutchison/tidyspatialexperiment/issues

Datasets:

demo_brush_data - Demo brush data
demo_select_data - Demo select data

On BioConductor:tidySpatialExperiment-1.3.0(bioc 3.21)tidySpatialExperiment-1.2.0(bioc 3.20)

infrastructure rnaseq geneexpression sequencing spatial transcriptomics singlecell

6.03 score 5 stars 12 scripts 166 downloads 5 exports 112 dependencies

Last updated 23 days agofrom:317a6d5eee. Checks:OK: 3 NOTE: 1 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:aggregate_cells ellipse gate rectangle unnest_single_cell_experiment

Dependencies:abind askpass base64enc Biobase BiocFileCache BiocGenerics bit bit64 blob bslib cachem cli colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest dplyr ellipsis evaluate fansi farver fastmap filelock fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plotly promises purrr R6 rappdirs RColorBrewer Rcpp rjson rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales shiny SingleCellExperiment sourcetools SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys tibble tidygate tidyr tidyselect tidySingleCellExperiment tinytex ttservice UCSC.utils utf8 vctrs viridis viridisLite withr xfun xtable XVector yaml zlibbioc

Overview

William Hutchison, Stefano Mangiola

Rendered fromoverview.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-07-13
Started: 2023-06-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Count the observations in each group	add_count add_count.SpatialExperiment count
Aggregate cells	aggregate_cells
Order rows using column values	arrange
Coerce lists, matrices, and more to data frames	as_tibble as_tibble.SpatialExperiment
Efficiently bind multiple data frames by row and column	bind_cols bind_cols.SpatialExperiment
Efficiently bind multiple data frames by row and column	bind_rows bind_rows.SpatialExperiment
Demo brush data	demo_brush_data
Demo select data	demo_select_data
Keep distinct/unique rows	distinct
Ellipse Gating Function	ellipse
Extract a character column into multiple columns using regular expression groups	extract extract.SpatialExperiment
Keep rows that match a condition	filter filter.SpatialExperiment
Printing tibbles	formatting print print.SpatialExperiment
Interactively gate cells by spatial coordinates	gate
Gate interactive	gate_interactive
Gate spatial data with pre-recorded lasso selection coordinates	gate_programmatic
Create a new 'ggplot' from a 'tidySpatialExperiment'	ggplot
Get a glimpse of your data	glimpse
Group by one or more variables	group_by
Mutating joins	inner_join inner_join.SpatialExperiment
Extract and join information for features.	join_features
Mutating joins	left_join left_join.SpatialExperiment
Create, modify, and delete columns	mutate mutate.SpatialExperiment
Nest rows into a list-column of data frames	nest nest.SpatialExperiment
Pivot data from wide to long	pivot_longer
Initiate a plotly visualization	plot_ly plot_ly.SpatialExperiment
Extract a single column	pull
Rectangle Gating Function	rectangle
Rename columns	rename
Mutating joins	right_join right_join.SpatialExperiment
Group input by rows	rowwise
Sample n rows from a table	sample_frac sample_frac.SpatialExperiment sample_n sample_n.SpatialExperiment
Keep or drop columns using their names and types	select select.SpatialExperiment
Separate a character column into multiple columns with a regular expression or numeric locations	separate separate.SpatialExperiment
Subset rows using their positions	slice slice_head slice_max slice_min slice_sample slice_tail
Summarise each group down to one row	summarise summarize
Format the header of a tibble	tbl_format_header tbl_format_header.tidySpatialExperiment
Unite multiple columns into one by pasting strings together	unite unite.SpatialExperiment
Unnest a list-column of data frames into rows and columns	unnest unnest.tidySpatialExperiment_nested unnest_single_cell_experiment