Package: ijAnalysis 0.0.4

ijAnalysis: Miscellaneous tools for image analysis tasks

A miscellaneous toolbox for various image analysis tasks. Initially contains tools for downstream analysis of my ImageJ plugin Puncta Tracker and hence the ij name. Part of the y3628 analysis suite.

Authors:Ye Yuan [aut, cre]

ijAnalysis_0.0.4.tar.gz
ijAnalysis_0.0.4.zip(r-4.7-any)ijAnalysis_0.0.4.zip(r-4.6-any)ijAnalysis_0.0.4.zip(r-4.5-any)
ijAnalysis_0.0.4.tgz(r-4.6-any)ijAnalysis_0.0.4.tgz(r-4.5-any)
ijAnalysis_0.0.4.tar.gz(r-4.7-any)ijAnalysis_0.0.4.tar.gz(r-4.6-any)
ijAnalysis_0.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ijAnalysis/json (API)

# Install 'ijAnalysis' in R:

install.packages('ijAnalysis', repos = c('https://yeyuan98.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yeyuan98/ijanalysis/issues

On CRAN:

2.00 score 1 scripts 21 exports 56 dependencies

Last updated from:d8a47c4d5d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	142
source / vignettes	OK	221
linux-release-x86_64	OK	143
macos-release-arm64	OK	77
macos-oldrel-arm64	OK	89
windows-devel	OK	77
windows-release	OK	75
windows-oldrel	OK	70
wasm-release	OK	118

Exports:actogram_loadFromMetadata actogram_plot ctcf_plot ctcf_read_csv ij_nnd.compute ij_RoiPointsSaver jtk.init jtkdist jtkget jtkx nlsGroup periodogram_loadClocklab plot_ggsave rfish_count rfish_read_dots rfish_read_samples spotInRoi_addMeta spotInRoi_as.data.frame.df.nnd spotInRoi_nnd.sort spotInRoi_read_csv spotInRoi_selectNCT

Dependencies:behavr bit bit64 cellranger cli clipr cpp11 crayon damr data.table dplyr farver generics ggetho ggplot2 glue gtable here hms isoband jsonlite labeling lattice lifecycle magrittr Matrix pillar pkgconfig png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppTOML readr readxl rematch reticulate rlang rprojroot S7 scales stringi stringr tibble tidyselect tzdb utf8 vctrs viridisLite vroom withr y3628

spotInRoi

What is spotInRoi analysis | The example dataset | Workflow

Rendered fromspotInRoi.Rmdusingknitr::rmarkdown

Last update: 2024-09-10
Started: 2024-08-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Parse spot array JSON data to metaRcrd.	.parse_meta
Get index for spotInRoi nuclear/full-cell data subsetting.	.selectNCT.index
Load behavior activity data from metadata	actogram_loadFromMetadata
Plotting actogram	actogram_plot
Load behavior metadata	behavior_loadMetadata
Standardized plotting of CTCF data	ctcf_plot
Read CTCF results table	ctcf_read_csv
Compute NND metrics for a pair of spot sets.	ij_nnd.compute
Initialize an ImageJ ROI point set saver function	ij_RoiPointsSaver
JTK Cycle V3.1 Adaptation 'jtk.init'	jtk.init
JTK Cycle V3.1 Adaptation 'jtkdist'	jtkdist
JTK Cycle V3.1 Adaptation	jtkget
JTK Cycle V3.1 Adaptation 'jtkstat'	jtkstat
JTK Cycle V3.1 Adaptation 'jtkx'	jtkx
'nls()' fitting of multiple groups	nlsGroup
Order permutation for a NND result record	nnd.order
Load Clocklab periodogram batch export table	periodogram_loadClocklab
Simple wrapper of ggsave for saving plots.	plot_ggsave
Boxplot with data points	plot.boxPoint
Point plot with lines connecting 'mean' values.	plot.linePoint
Standardized themes for plotting	plot.themes
Count number of dots per cell	rfish_count
Read dots table from snakemake pipeline output	rfish_read_dots
Read samples table from snakemake pipeline output	rfish_read_samples
Add metadata column to spotInRoi data	spotInRoi_addMeta
Expand NND results as data frame entries	spotInRoi_as.data.frame.df.nnd
Join spotInRoi data with metadata columns	spotInRoi_joinMeta
Sort spotInRoi data based on NND results	spotInRoi_nnd.sort
Read data for spotInRoi analysis of the Puncta Tracker ImageJ plugin.	spotInRoi_read_csv
Predefined subsetting of spotInRoi nuclear/full-cell data.	spotInRoi_selectNCT
Simple subset of 'behavr::behavr' behavior tables	subset_behavr