Meta_St_img_unsupervised: Title

In ShanYiran/TIST: TIST， Transcritpome and histopathological Image integrative analysis for Spatial Transcriptomics

Title

Description

Title

Usage

Meta_St_img_unsupervised(
  Maskfile,
  imagefile,
  exprPath,
  SC_obj = NULL,
  spaceFile,
  colors = NULL,
  savePath,
  Method = "walktrap",
  imgMethod = "Marcov",
  imginitMethod = "Kmeans",
  Step = NULL,
  spot_r_min = 12,
  spot_r_max = 20,
  cluster_num = 50,
  maxiter = 10,
  sacle_score = 0.09920635,
  img_import = 1
)

Arguments

Maskfile	The address where the Mask file is stored. Such as "/home/data/Imginit/mask.txt". You can use no mask to generate an all 1 matrix. The more recommended approach is generate this mask file use our python code in this package.
imagefile	The address where the Image file is stored. Such as "/home/data/spatial/tissue_hires_image.png".
exprPath	The address where the RNA-seq file is stored. Such as "/home/data/filtered_feature_bc_matrix/".
SC_obj	If exprPath is NULL, you can also load RNA-seq use an existed Seruat object. Default is NULL.
spaceFile	The address where the local file of all spots is stored. Such as "spatial/tissue_positions_list.csv".
colors	Color bar for visualization. We will give a default color scheme if NULL.
savePath	The address where the results stored.
Method	The Network-based methods to find clusters. Default param is walktrap,
imgMethod	The image feather select method. Default is Marcov, Other optional: Kmeans. We will use original image feature if NULL.
imginitMethod	If imgMethod is Marcov, this param is to select label init method, such as "Kmeans" default or "Random".
Step	Control the step length of random walk for walkstrap method.
spot_r_min	A min window to select Image features. Default is 12.
spot_r_max	A max window to select Image features. Default is 20.
cluster_num	The number of init cluster for image. Default is 50.
maxiter	The number of iterations for marcov. Default is 10.
sacle_score	The scale to map the spots coordinate in spaceFile with image.
img_import	The image feature weight for feature integration.

Value

TIST results.

Examples

  Spot_manifest_imgunsup <- Meta_St_img_unsupervised(Maskfile = Maskfile,
  imagefile = imagefile,
  spaceFile = spaceFile,
  exprPath = exprPath,
  colors = NULL,
  savePath = savePath,
  Method = "walktrap",
  sacle_score = sacle_score)

ShanYiran/TIST documentation built on July 22, 2022, 11:48 p.m.