Alberto Fabbri
Alberto Fabbri
Hi, thank you for this nice package! I generated a heatmap using the following code: ``` netVisual_heatmap( object = cellchat, measure = "count", # Darker color for interactions close to...
Hi, I have performed an analysis using the Cell-Cell Contact, Secreted Signaling, and ECM-Receptor interaction categories from the CellChat database.  ### Goal I would like to generate visualizations of...
I am using CosMx for my analysis and it is not entirely clear to me what is the spot size. The documentation states: _tol: the tolerance factor to increase the...
The CellChat document [Frequently Asked Questions when analyzing spatially resolved transcriptomics datasets](https://htmlpreview.github.io/?https://github.com/jinworks/CellChat/blob/master/tutorial/FAQ_on_applying_CellChat_to_spatial_transcriptomics_data.html) states: _For CosMx data, the spatial coordinates are in pixels and the conversion factor of converting spatial coordinates...
Hi, it is my first time using CellChat and I was wondering what is the correct approach to analyze a TMA. I have the following slide as a single image...
Hi, when running the following code: ``` conversion.factor = 0.18 d = computeCellDistance( coordinates = spatial.locs, # to convert the distance from pixels to micrometers ratio = conversion.factor) median_cell_distance =...
Hi 👋, I’d like to suggest a feature that would make `facet_col()` more flexible: adding a data parameter, similar to how it works in `ggplot()` or `geom_*()` layers. ## Motivation...
I think the `slot` parameter in `DoHeatmap` should be deprecated in favor of `layer`.
Hi and thank you for developing and maintaining CellChat! I noticed that adding the metadata column `samples` to the CellChat object affects the number of detected cell–cell communications even when...
Hi, I am analyzing data from a targeted gene panel (CosMx/Nanostring) using CellChat. Since many ligands and receptors in `CellChatDB` are not included in my panel, I am considering filtering...