pachterlab/voyager

Issues

• Question re: running local moran I with different graph types / spot dropout

  #40 opened 11 days ago by spcdot
  2

• New argument(s) in plotSpatialFeature to selectively plot cells or spots

  #39 opened 12 days ago by lambdamoses
  0

• Clean up how parameters used to compute graphs and spatial stats are stored

  #38 opened 21 days ago by lambdamoses
  0

• Plot rowGeometries

  #14 opened 4 months ago by lambdamoses
  10

• Refactor `SFEMethods` to be more like `BlusParam`

  #17 opened 4 months ago by lambdamoses
  0

• how to change color of plotLocalResult (remain spots with p < 0.05 only)

  #35 opened 4 months ago by huiyijiangling
  2

• Update Xenium vignette to use flagship data rather than prototype

  #9 opened 4 months ago by lambdamoses
  0

• 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

  #37 opened 4 months ago by huiyijiangling
  2

• Vignette using multiple samples

  #25 opened 9 months ago by lambdamoses
  2

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

  #36 opened 4 months ago by huiyijiangling
  1

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

  #34 opened 5 months ago by huiyijiangling
  1

• proseg output support

  #32 opened 6 months ago by cstrlln
  10

• make VisiumHD vignettes

  #33 opened 6 months ago by alikhuseynov
  0

• Plotting function just to show images without geometries

  #29 opened 7 months ago by lambdamoses
  0

• Plot multiple grayscale images at once as different channels in `plotSpatialFeature` and related functions

  #19 opened 7 months ago by lambdamoses
  0

• Allow users to select any channel in images in plotting functions

  #20 opened 7 months ago by lambdamoses
  0

• Support `BioFormatsImage` and `EBImage` in `plotSpatialFeature`

  #26 opened 7 months ago by lambdamoses
  1

• Move colFeatureData and related functions to SFE package

  #10 opened 8 months ago by lambdamoses
  1

• Vignette about multi-scale analyses

  #31 opened 8 months ago by lambdamoses
  0

• Add argument to `plotSpatialFeature` for whether to show axes

  #28 opened 8 months ago by lambdamoses
  0

• Option to plot only polygon outlines without fill in `plotColGeometry`

  #22 opened 8 months ago by lambdamoses
  0

• Joint count vignette

  #30 opened 8 months ago by lambdamoses
  0

• Option to plot image in a separate adjacent panel rather than behind cells/spots

  #21 opened 10 months ago by lambdamoses
  0

• Vignette for Tomo-seq

  #27 opened 9 months ago by lambdamoses
  0

• Specify whether bivariate method in `SFEMethod` class is symmetric

  #18 opened 10 months ago by lambdamoses
  0

• Write alt text for vignette figures

  #24 opened 9 months ago by lambdamoses
  0

• Plot scale bar when unit = "micron"

  #23 opened 9 months ago by lambdamoses
  0

• Error when bbox is used

  #16 opened a year ago by alikhuseynov
  3

• Matrix >= 1.6.2 breaks Voyager

  #15 opened a year ago by rsbivand
  2

• error in `geom_spi_rgb()` when using ` image_id` in `plotSpatialFeature()`

  #11 opened a year ago by alikhuseynov
  7

• Polygon boundaries showing despite linewidth = 0 in `plotSpatialFeature` on Windows

  #13 opened a year ago by lambdamoses
  0

• Can't plot spatial graph for one out of multiple samples

  #12 opened a year ago by lambdamoses
  0

• Voyager utility

  #8 opened a year ago by chrkuo
  1

• References on documentation website

  #7 opened a year ago by lambdamoses
  0

• could not find function "calculateBivariate"

  #4 opened 2 years ago by gakabani
  14

• Transposing SFE object gets image and spots out of alignment

  #5 opened 2 years ago by lambdamoses
  1

• plotColDataHistogram doesn't allow illegal symbols

  #6 opened 2 years ago by lambdamoses
  0

• read/load image-based spatial transcriptomics

  #2 opened 2 years ago by alikhuseynov
  18

• Forthcoming spdep release seems to break Voyager

  #3 opened 2 years ago by rsbivand
  3