pachterlab / voyager

From geospatial to spatial -omics

https://pachterlab.github.io/voyager/

pachterlab/voyager Issues

Errors in calculateBivariate:check_Ops_vector_arg_length(e, x_nrow, e_what = e_what, x_what = x_what): when the right operand is not a DelayedArray object (or derivative), its length cannot be greater than the first dimension of the left operand
Updated 16 days ago
Local bivariate Moran's l (-log10p_adj Sim) look the same
Updated 16 days ago
how to change color of plotLocalResult (remain spots with p < 0.05 only)
Updated 16 days ago1
A bug of Blank plots in workflow: Seurat V5 (with image) ->toSpatialFeatureExperiment -> plotSpatialFeature
Updated 17 days ago1
proseg output support
Updated a month ago10
make VisiumHD vignettes
Updated 2 months ago
Refactor `SFEMethods` to be more like `BlusParam`
Updated 2 months ago
Plotting function just to show images without geometries
Closed 3 months ago
Plot multiple grayscale images at once as different channels in `plotSpatialFeature` and related functions
Closed 3 months ago
Allow users to select any channel in images in plotting functions
Closed 3 months ago
Support `BioFormatsImage` and `EBImage` in `plotSpatialFeature`
Closed 3 months ago1
Move colFeatureData and related functions to SFE package
Closed 4 months ago1
Vignette about multi-scale analyses
Updated 4 months ago
Plot rowGeometries
Updated 4 months ago8
Add argument to `plotSpatialFeature` for whether to show axes
Closed 4 months ago
Option to plot only polygon outlines without fill in `plotColGeometry`
Closed 4 months ago
Joint count vignette
Updated 4 months ago
Option to plot image in a separate adjacent panel rather than behind cells/spots
Updated 4 months ago
Vignette for Tomo-seq
Updated 5 months ago
Update Xenium vignette to use flagship data rather than prototype
Updated 5 months ago
Vignette using multiple samples
Updated 5 months ago
Specify whether bivariate method in `SFEMethod` class is symmetric
Updated 5 months ago
Write alt text for vignette figures
Updated 5 months ago
Plot scale bar when unit = "micron"
Updated 5 months ago
Error when bbox is used
Closed 7 months ago3
Matrix >= 1.6.2 breaks Voyager
Closed 7 months ago2
error in `geom_spi_rgb()` when using ` image_id` in `plotSpatialFeature()`
Closed 10 months ago7
Polygon boundaries showing despite linewidth = 0 in `plotSpatialFeature` on Windows
Closed 10 months ago
Can't plot spatial graph for one out of multiple samples
Closed 10 months ago
Voyager utility
Closed a year ago1
References on documentation website
Closed a year ago
could not find function "calculateBivariate"
Closed a year ago14
Transposing SFE object gets image and spots out of alignment
Closed a year ago1
plotColDataHistogram doesn't allow illegal symbols
Closed a year ago
read/load image-based spatial transcriptomics
Closed a year ago18
Forthcoming spdep release seems to break Voyager
Closed a year ago3