pachterlab/voyager issues and pull requests

#38 - Clean up how parameters used to compute graphs and spatial stats are stored

Issue - State: open - Opened by lambdamoses 24 days ago

#37 - 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

Issue - State: closed - Opened by huiyijiangling 5 months ago - 2 comments
Labels: bug

#36 - Local bivariate Moran's l (-log10p_adj Sim) look the same

Issue - State: closed - Opened by huiyijiangling 5 months ago - 1 comment

#35 - how to change color of plotLocalResult (remain spots with p < 0.05 only)

Issue - State: closed - Opened by huiyijiangling 5 months ago - 2 comments

#34 - A bug of Blank plots in workflow: Seurat V5 (with image) ->toSpatialFeatureExperiment -> plotSpatialFeature

Issue - State: open - Opened by huiyijiangling 5 months ago - 1 comment

#33 - make VisiumHD vignettes

Issue - State: open - Opened by alikhuseynov 6 months ago

#32 - proseg output support

Issue - State: open - Opened by cstrlln 7 months ago - 10 comments

#31 - Vignette about multi-scale analyses

Issue - State: open - Opened by lambdamoses 8 months ago
Labels: documentation, enhancement

#30 - Joint count vignette

Issue - State: open - Opened by lambdamoses 8 months ago
Labels: documentation, enhancement

#29 - Plotting function just to show images without geometries

Issue - State: closed - Opened by lambdamoses 8 months ago
Labels: enhancement, plotting

#28 - Add argument to `plotSpatialFeature` for whether to show axes

Issue - State: closed - Opened by lambdamoses 9 months ago
Labels: enhancement, plotting, intermediate

#27 - Vignette for Tomo-seq

Issue - State: open - Opened by lambdamoses 9 months ago
Labels: documentation, intermediate

#26 - Support `BioFormatsImage` and `EBImage` in `plotSpatialFeature`

Issue - State: closed - Opened by lambdamoses 9 months ago - 1 comment
Labels: enhancement, advanced, plotting

#25 - Vignette using multiple samples

Issue - State: open - Opened by lambdamoses 9 months ago - 2 comments
Labels: documentation, enhancement, advanced

#24 - Write alt text for vignette figures

Issue - State: open - Opened by lambdamoses 9 months ago
Labels: documentation, beginner

#23 - Plot scale bar when unit = "micron"

Issue - State: open - Opened by lambdamoses 9 months ago
Labels: enhancement, plotting, intermediate

#22 - Option to plot only polygon outlines without fill in `plotColGeometry`

Issue - State: closed - Opened by lambdamoses 10 months ago
Labels: enhancement, plotting, beginner

#21 - Option to plot image in a separate adjacent panel rather than behind cells/spots

Issue - State: open - Opened by lambdamoses 10 months ago
Labels: enhancement, plotting, intermediate

#20 - Allow users to select any channel in images in plotting functions

Issue - State: closed - Opened by lambdamoses 10 months ago
Labels: enhancement, advanced, plotting

#19 - Plot multiple grayscale images at once as different channels in `plotSpatialFeature` and related functions

Issue - State: closed - Opened by lambdamoses 10 months ago
Labels: enhancement, advanced, plotting

#18 - Specify whether bivariate method in `SFEMethod` class is symmetric

Issue - State: open - Opened by lambdamoses 10 months ago
Labels: enhancement, advanced

#17 - Refactor `SFEMethods` to be more like `BlusParam`

Issue - State: closed - Opened by lambdamoses 10 months ago
Labels: wontfix

#16 - Error when bbox is used

Issue - State: closed - Opened by alikhuseynov 12 months ago - 3 comments

#15 - Matrix >= 1.6.2 breaks Voyager

Issue - State: closed - Opened by rsbivand about 1 year ago - 2 comments

#14 - Plot rowGeometries

Issue - State: closed - Opened by lambdamoses about 1 year ago - 10 comments
Labels: enhancement, plotting, intermediate

#13 - Polygon boundaries showing despite linewidth = 0 in `plotSpatialFeature` on Windows

Issue - State: closed - Opened by lambdamoses about 1 year ago

#12 - Can't plot spatial graph for one out of multiple samples

Issue - State: closed - Opened by lambdamoses about 1 year ago

#11 - error in `geom_spi_rgb()` when using ` image_id` in `plotSpatialFeature()`

Issue - State: closed - Opened by alikhuseynov about 1 year ago - 7 comments

#10 - Move colFeatureData and related functions to SFE package

Issue - State: closed - Opened by lambdamoses over 1 year ago - 1 comment
Labels: intermediate, refactor

#9 - Update Xenium vignette to use flagship data rather than prototype

Issue - State: closed - Opened by lambdamoses over 1 year ago
Labels: documentation, intermediate

#8 - Voyager utility

Issue - State: closed - Opened by chrkuo over 1 year ago - 1 comment

#7 - References on documentation website

Issue - State: closed - Opened by lambdamoses over 1 year ago

#6 - plotColDataHistogram doesn't allow illegal symbols