Package: tidySpatialExperiment 1.9.0

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]

tidySpatialExperiment_1.9.0.tar.gz
tidySpatialExperiment_1.9.0.zip(r-4.7)tidySpatialExperiment_1.9.0.zip(r-4.6)tidySpatialExperiment_1.9.0.zip(r-4.5)
tidySpatialExperiment_1.9.0.tgz(r-4.6-any)tidySpatialExperiment_1.9.0.tgz(r-4.5-any)
tidySpatialExperiment_1.9.0.tar.gz(r-4.7-any)tidySpatialExperiment_1.9.0.tar.gz(r-4.6-any)
tidySpatialExperiment_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tidySpatialExperiment/json (API)

# 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

Pkgdown/docs site:https://william-hutchison.github.io

Datasets:

demo_brush_data - Demo brush data
demo_select_data - Demo select data

On BioConductor:tidySpatialExperiment-1.9.0(bioc 3.24)tidySpatialExperiment-1.8.0(bioc 3.23)

infrastructure rnaseq geneexpression sequencing spatial transcriptomics singlecell

6.53 score 8 stars 1 packages 19 scripts 394 downloads 4 exports 105 dependencies

Last updated from:67d77f3ade. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	218
linux-devel-x86_64	OK	417
source / vignettes	OK	308
linux-release-x86_64	OK	376
macos-release-arm64	OK	220
macos-oldrel-arm64	OK	240
windows-devel	OK	289
windows-release	OK	290
windows-oldrel	OK	325
wasm-release	OK	186

Exports:aggregate_cells ellipse gate rectangle

Dependencies:abind askpass base64enc Biobase BiocFileCache BiocGenerics bit bit64 blob bslib cachem cli commonmark cpp11 crosstalk curl data.table DBI dbplyr DelayedArray digest dplyr ellipsis evaluate fansi farver fastmap filelock fontawesome fs generics GenomicRanges ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httpuv httr httr2 IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magick magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rjson rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales Seqinfo shiny SingleCellExperiment sourcetools SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys tibble tidygate tidyr tidyselect tidySingleCellExperiment tinytex ttservice utf8 vctrs viridis viridisLite withr xfun xtable XVector yaml

Overview

Rendered fromoverview.Rmdusingknitr::rmarkdown

Last update: 2024-09-24
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
Efficiently bind multiple data frames by row and column	bind_rows
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