Hotspots and help(SpaceMarkersFunction) #48
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… sigma (lowres as default). Incorperated changes from main branch intp SpaceMarkers_vignette including new plotting functions, getSpatialParametersExternal and getPairwiseInteractingGenes
…resolution scaling as specified in getSpatialParamsExternal.
…changed kernelthreshold default from 3 to 4. c) Exported findPatternHotspots function d) Added examples and tests in testthat 2. Updated functions' documentation for cleaner and more readable text in R's help menu
| @@ -1,13 +1,75 @@ | |||
| ## author: Atul Deshpande | |||
| ## email: [email protected] | |||
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| find_pattern_hotspots <- function( | |||
| #=================== | |||
| #' @title Calculate influence of spatially varying features | |||
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Identify hotspots of spatial pattern influence
dimalvovs
reviewed
Nov 18, 2024
| @@ -1,13 +1,75 @@ | |||
| ## author: Atul Deshpande | |||
| ## email: [email protected] | |||
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| find_pattern_hotspots <- function( | |||
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Great, it's comforting to see we're getting back to harmonized fun names
dimalvovs
reviewed
Nov 18, 2024
| spPatterns, params = NULL, patternName = "Pattern_1", | ||
| outlier = "positive", | ||
| nullSamples = 100, includeSelf = TRUE,...){ | ||
| if (is.null(params)){ | ||
| sigmaPair <- 10 | ||
| kernelthreshold <- 3 | ||
| kernelthreshold <- 4 |
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Just curious, why not 5?
dimalvovs
reviewed
Nov 18, 2024
| if (!all(patternPairs %in% patternList)) | ||
| stop("Following are not pattern names: ", | ||
| paste0(setdiff(patternPairs, patternList)," ")) | ||
| stop("Following are not pattern names: ",mess ) |
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stop mess :) (just noticing, no call to action)
dimalvovs
reviewed
Nov 18, 2024
| @@ -139,10 +135,12 @@ getSpatialParameters <- function(spatialPatterns,...){ | |||
| #' @param spatialDir A string path specifying the location of the spatial folder | |||
| #' containing the .json file of the spot characteristics | |||
| #' @param pattern A string specifying the name of the .json file | |||
| #' @param spotDiameter A numeric value specifying your desired sigma | |||
| #' @param sigma A numeric value specifying your desired sigma | |||
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I'd rather note what sigma is and how it affects the result instead of kind of obvious "A numeric value specifying your desired sigma"
dimalvovs
reviewed
Nov 18, 2024
| @@ -19,11 +19,11 @@ test_that("getInteracting genes return empty interacting_genes object when no in | |||
| "Pattern_2" = runif(cell_num , min=0, max=1)) | |||
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| optParams <- NULL | |||
| output <- getInteractingGenes(data=data, spPatterns, reconstruction=NULL, | |||
| suppressWarnings(output <- getInteractingGenes(data=data, spPatterns, reconstruction=NULL, | |||
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What is warning that we suppress here? Do we risk suppressing something unwanted?
dimalvovs
reviewed
Nov 18, 2024
| tissue_hires_scalef = 2, | ||
| tissue_lowres_scalef = 3, | ||
| tissue_hires_scalef = 0.75, | ||
| tissue_lowres_scalef = 0.25, | ||
| spot_diameter_fullres = 4 |
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Just noticing - if we changed the spotDiameter to sigma elsewhere, do we need to do the same also here?
dimalvovs
approved these changes
Nov 18, 2024
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Looks OK to me, just 3 things maybe to consider
- spotDiameter change to sigma: I can't really understand what sigma is, and how it affects the results;
- supressWarnings: can it be that we'll suppress something important? What we're suppressing by the way?
- spotDiameter changed to sigma in the fun, but not in the json_data, it it OK?
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Hotspots:
a) Change find_pattern_hotspots to camel case findPatternHotspots.
b) changed kernelthreshold default from 3 to 4.
c)Exported findPatternHotspots function
d) Added examples and tests in testthat
Updated SpaceMarkers functions description for more readable titles in R help menu. Did not make changes to the actual functions
Removed files associated with getSpatialParametersExternal and replaced with getSpatialParamsExternal