update_feature: Update aSVG Spatial Features

In jianhaizhang/spatialHeatmap: spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Update aSVG Spatial Features

Description

Successful spatial heatmap plotting requires the aSVG features of interest have matching samples (cells, tissues, etc) in the data. If this requirement is not fulfiled, either the sample identifiers in the data or the spatial feature identifiers in the aSVG should be changed. This function is designed to replace existing feature identifiers, stroke (outline) widths, and/or feature colors in aSVG files with user-provided entries.

Usage

update_feature(df.new, dir)

Arguments

df.new

The custom feature identifiers, stroke (outline) widths, and/or feature colors, should be included in the data frame returned by return_feature as independent columns, and the corresponding column names should be "featureNew", "strokeNew", and "colorNew" respectively in order to be recognized. To color the corresponding features, the identifiers in "featureNew" should be the same with matching sample identifiers. The numeric values in "strokeNew" would be the outline widths of corresponding features. The colors in "colorNew" would be the default colors for highlighting target features in the legend plot.

dir

The directory path where the aSVG files to update. It should be the same with dir in return_feature.

Value

Nothing is returned. The aSVG files of interest in dir are updated with provided attributes, and are ready to use in function spatial_hm.

Author(s)

Jianhai Zhang [e-mail]
Dr. Thomas Girke [e-mail]

References

Hadley Wickham, Jim Hester and Jeroen Ooms (2019). xml2: Parse XML. R package version 1.2.2. https://CRAN.R-project.org/package=xml2 Cardoso-Moreira, Margarida, Jean Halbert, Delphine Valloton, Britta Velten, Chunyan Chen, Yi Shao, Angélica Liechti, et al. 2019. "Gene Expression Across Mammalian Organ Development." Nature 571 (7766): 505-9 Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber, Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz and Bill Venables (2020). gplots: Various R Programming Tools for Plotting Data. R package version 3.0.3. https://CRAN.R-project.org/package=gplots

Examples

# The following shows how to download a chicken aSVG containing spatial features of 'brain'
# and 'heart' from the EBI aSVG repository directly 
# (https://github.com/ebi-gene-expression-group/anatomogram/tree/master/src/svg). An empty
# directory is recommended so as to avoid overwriting existing SVG files with the same names.
# Here "~/test" is used. 

# Remote aSVG repos.
data(aSVG.remote.repo)
tmp.dir <- normalizePath(tempdir(check=TRUE), winslash="/", mustWork=FALSE)
tmp.dir.ebi <- paste0(tmp.dir, '/ebi.zip')
tmp.dir.shm <- paste0(tmp.dir, '/shm.zip')

# Download the remote aSVG repos as zip files. According to Bioconductor's 
# requirements, downloadings are not allowed inside functions, so the repos are 
# downloaded before calling "return_feature".  
download.file(aSVG.remote.repo$ebi, tmp.dir.ebi)
download.file(aSVG.remote.repo$shm, tmp.dir.shm)
remote <- list(tmp.dir.ebi, tmp.dir.shm)
# Make an empty directory "~/test" if not exist.
if (!dir.exists('~/test')) dir.create('~/test')
# Query the remote aSVG repos.
feature.df <- return_feature(feature=c('heart', 'brain'), species=c('gallus'), dir='~/test',
match.only=TRUE, remote=remote)
feature.df

# New features, stroke widths, colors.
ft.new <- c('BRAIN', 'HEART')
stroke.new <- c(0.05, 0.1)
col.new <- c('green', 'red')
# Include new features, stroke widths, colors to the feature data frame.
feature.df.new <- cbind(featureNew=ft.new, strokeNew=stroke.new, colorNew=col.new, feature.df)
feature.df.new

# Update features.
update_feature(df.new=feature.df.new, dir='~/test')

jianhaizhang/spatialHeatmap documentation built on Nov. 28, 2024, 4:44 p.m.