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View Code? Open in Web Editor NEWR package to visualize colocalization for single cell & spatially-resolved genomics data
Home Page: https://boyi-guo.com/escheR/
License: Other
R package to visualize colocalization for single cell & spatially-resolved genomics data
Home Page: https://boyi-guo.com/escheR/
License: Other
Here are some suggestion on improving the clarity of documentation from @cindyfang70.
reverse_y
escheR
vigenette.Thanks @cindyfang70 for the feedback!
Suggested by Byron Jaeger.
Current code default the names for the spatialCoords to be "pxl_row_in_fullres", "pxl_col_in_fullres" without giving a warning.
Need to have more flexible implementation.
n <- length(z <- letters)
y <- matrix(nrow = n, ncol = n)
cd <- DataFrame(x = seq(n), y = seq(n), z)
spe1 <- SpatialExperiment(
assay = y,
colData = cd,
spatialCoordsNames = c("x", "y"))
THere are error message that has not been updated
Error in make_escheR.SpatialExperiment(spe[, spe$sample_id %in% c("V13M06-342_D1")]) :
make_escheR currently only supports spe object with 1 sample. Please find tips multiple sample plots in [TODO] vignettes.
Contributor: @Erik-D-Nelson
A function to normalize continuous variables to RGB color space
A case study applying this concept to a Visium dataset
if (!exists("spe"))
spe <- fetch_data("spatialDLPFC_Visium")
Thank you for submition your package to Bioconductor. The package passed check and build. It is in pretty good shape. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review.
Code: Note: please condsider; Important: must be addressed.
Response: Added R(>=3.6) as dependency
importFrom
instead of import all with import
.
Response: Imported individual functions instead of entire packages
paste
in message()
, message
, stop
Response: removed all
paste
functions instop
etc. Thanks for this tip.
::
is not suggested in source code unless you can make sure all the packages are imported. Some people think it is better to keep ::
. However please note that you need to manully double check the import items when you make any change in the DESCRIPTION file during development. My recommendation is to remove one or two repeats to force the dependency check.
Response: Thank you very much for this information. I followed your suggestion to make some functions without
::
such that the source code for the dependency check. But I would still like to leave some of them in the code to enhance readability for people who are not familiar with these packages. Thanks for sharing this trick!
1:n
is not suggested in source code. Use seq_along
or seq.int
instead.
Response: removed the commented code and hence this line. But I will be more careful with my coding practice to use
seq.int
etc instead of1:n
. Thank you for this tip!
Response: removed the commented code.
Response: removed the commented code. But I will be more careful with the practice in general in the future. Thank you for this tip!
add_fill
and add_ground
and add_symbol
Response: Thank you for the suggestion! I am aware of this situation, and currently working on a
check_var
function for this purpose and some more checks. This improvement will be fully implemented in the next update of the package.
theme
in function make_escheR.SpatialExperiment
to a sub_function.Response: Thank you for the suggestion! I'll reserve this as an option in the next update of the package.
dots
to pass parameters to geom_point
in add_symbol
function and add_fill
function and let user to overwrite the defaults.Response: Thank you for the suggestion! I had a similar idea, but I would like to have some more time to think about the design of this function. I will prioritize this tasks in the next update of this package.
Response: Added BiocManager installation instructions
motivation for submitting to Bioconductor
as part of the abstract/intro of the main vignette.
Response: Remove mentioning of Bioconductor submission
Originally posted by @jianhong in Bioconductor/Contributions#2988 (comment)
As noted in the vignette Beyond Sequence-based Spatially-Resolved Data, the binning strategy proposed to address overplotting could lead to distorted interpretation due intermixing of data points within each bin.
A possible solution to address this is to display the proportion of majority membership within each bin using either transparency (alpha
) or boundary size (stroke
).
Hello!
I am trying to change the spot size of the points using the example you have online but have been unable to do so. See below the code I am running.. is there something I am doing wrong? Thanks so much!
library(STexampleData)
spe <- Visium_humanDLPFC()
make_escheR(spe, spot_size=0.1) |> add_fill(var = "in_tissue")
make_escheR(spe, spot_size=5) |> add_fill(var = "in_tissue")
make_escheR(spe, spot_size=10) |> add_fill(var = "in_tissue")
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