Use bancr:: to reference package's own data when used in function

R/ggplot2.R

@@ -56,9 +56,9 @@ banc_neuron_comparison_plot <- function(neuron1,
   check_package_available('ggpubr')
   glist <- list()
   title.col <- "black"
-  if(is.null(banc_brain_neuropil)) {utils::data("banc_brain_neuropil.surf", envir = environment()); banc_brain_neuropil <- banc_brain_neuropil.surf}
-  if(is.null(banc_vnc_neuropil)) {utils::data("banc_brain_neuropil.surf", envir = environment()); banc_vnc_neuropil <- banc_vnc_neuropil.surf}
-  if(is.null(banc_neuropil)) {utils::data("banc_brain_neuropil.surf", envir = environment()); banc_neuropil <- banc_neuropil.surf}
+  if(is.null(banc_brain_neuropil)) {banc_brain_neuropil <- bancr::banc_brain_neuropil.surf}
+  if(is.null(banc_vnc_neuropil)) {banc_vnc_neuropil <- bancr::banc_vnc_neuropil.surf}
+  if(is.null(banc_neuropil)) {banc_neuropil <- bancr::banc_neuropil.surf}
   for(view in names(banc_rotation_matrices)){
 
     # Choose mesh

R/xform.R

@@ -386,15 +386,15 @@ banc_to_JRC2018F <- function(x,
   }else{
     if(inverse){
       # Result is in nm
-      utils::data("jrc2018f_to_banc_tpsreg", envir = environment())
+      # utils::data("jrc2018f_to_banc_tpsreg", envir = environment())
       xyz2 <- Morpho::applyTransform(xyz,
-                                     trafo = jrc2018f_to_banc_tpsreg,
+                                     trafo = bancr::jrc2018f_to_banc_tpsreg,
                                      inverse = FALSE)
     }else{
       # Result is in um
-      utils::data("banc_to_jrc2018f_tpsreg", envir = environment())
+      # utils::data("banc_to_jrc2018f_tpsreg", envir = environment())
       xyz2 <- Morpho::applyTransform(xyz,
-                                     trafo = banc_to_jrc2018f_tpsreg,
+                                     trafo = bancr::banc_to_jrc2018f_tpsreg,
                                      inverse = FALSE)
     }
   }
@@ -524,8 +524,9 @@ banc_mirror <- function(x,
     }
 
     # use pre-calculated tps reg
+    # utils::data("banc_mirror_tpsreg", envir = environment())
     x.banc.m <- Morpho::applyTransform(xyz,
-                                       trafo = utils::data("banc_mirror_tpsreg", envir = environment()))
+                                       trafo = bancr::banc_mirror_tpsreg)
 
     # convert from um to original banc.units if necessary
     if(banc.units=='um'){

README.md

@@ -4,15 +4,15 @@
 [![R-CMD-check](https://github.com/flyconnectome/banc/workflows/R-CMD-check/badge.svg)](https://github.com/flyconnectome/banc/actions)
 [![R-CMD-check](https://github.com/flyconnectome/bancr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/flyconnectome/bancr/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
-
+c
 bancr
 ===========
 
 The goal of **bancr** is to support analysis of the Brain And
 Nerve Cord dataset aka (*BANC*), especially autosegmentation data. 
 Those data are made available by the *BANC* project led by Wei-Chung Allen Lee (Harvard) 
 and collaborators including Zetta.ai and the FlyWire team at Princeton. 
-Anyon can request access to the data [here](https://flywire.ai/banc_access).
+Anyone can request access to the data [here](https://flywire.ai/banc_access).
 Learn more on the [BANC wiki](https://github.com/jasper-tms/the-BANC-fly-connectome/wiki/).
 
 To access banc resources, you must have permissions to access the [banc
@@ -356,6 +356,7 @@ And then get known *FAFB-FlyWire* neurons.
 # Which directs you towards the active FAFB-FlyWire segmentation
 
 # Define the IDs we wish to fetch
+# these are from the 783 materialisation (i.e.) published version
 fw.an1.ids <- c("720575940626768442", "720575940636821616")
 
 # Get neuron meshes
@@ -443,7 +444,7 @@ Acknowledgements
 ----------------
 
 The BANC data set was collected at Harvard Medical School in he laboratory of Wei-Chung Allen Lee, by Minsu Kim and Jasper Phelps.
-The segmentation and synapse prediction was built by [Zett.ai](https://zetta.ai/). 
+The segmentation and synapse prediction was built by [Zetta.ai](https://zetta.ai/). 
 The neuron reconstruction effort has been hosted and support by [FlyWire](https://flywire.ai/).
 This R package was built from principles developed
 by Greg Jefferis at the Laboratory of Molecular Biology.