plot_auto_largeImage_resample: Optimized largeImage resampling

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Optimized largeImage resampling

Description

Downsample largeImage for plotting. Uses spatSample to load only a portion of the original image, speeding up plotting and lowering memory footprint.

Default behavior of spatSample is to crop if only a smaller ROI is needed for plotting followed by the sampling process in order to reduce wasted sampling by focusing the sample space. For very large ROIs, this crop can be time intensive and require writing to disk.

This function examines the ROI dimensions as defined through the limits of the spatial locations to be plotted, and decides between the following two methods in order to avoid this issue:

• Method A. First crop original image and then sample n values where n = 500,000 to generate final image

• Method B. First oversample n values and then crop, where n = 500,000 scaled by a value >1. Scaling factor increases the smaller the ROI is and is defined by: original dimensions/crop dimensions where the larger ratio between x and y dims is chosen. Scale factor is capped by max_resample_scale

Control points for this function are set by max_crop which decides the max ROI area after which switchover to method B happens in order to avoid laborious crops and max_resample_scale which determines the maximum scale factor for number of values to sample. Both values can be adjusted depending on system resources. Additionally, flex_resample determines if this switching behavior happens. When set to FALSE, only method A is used.

Usage

plot_auto_largeImage_resample(
  gobject,
  giottoLargeImage = NULL,
  largeImage_name = NULL,
  spat_unit = NULL,
  spat_loc_name = NULL,
  polygon_feat_type = NULL,
  include_image_in_border = TRUE,
  flex_resample = TRUE,
  max_crop = 1e+08,
  max_resample_scale = 100
)

Arguments

gobject	gobject containing largeImage object
giottoLargeImage	largeImage object to resample if not provided through gobject and largeImage_name
largeImage_name	name of largeImage in gobject
spat_unit	spatial unit
spat_loc_name	name of spatial locations to plot
polygon_feat_type	name of polygon/spatial_info to plot
include_image_in_border	[boolean] expand the extent sampled to also show image in border regions not included in spatlocs. This prevents images in plots from being sharply cut off around the furthest spatial locations. (default is TRUE)
flex_resample	[boolean] Whether to allow automatic selection of sampling workflow as defined in details sections. (default is TRUE)
max_crop	maximum crop size allowed for method A before switching to method B (see description)
max_resample_scale	maximum cells allowed to resample to compensate for decreased resolution when cropping after sampling

Value

a giottoLargeImage cropped and resampled properly for plotting

See Also

spatSample

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.