Diffusion_net_analysis: Title

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

Title

Description

Title

Usage

Diffusion_net_analysis(
  SC_obj,
  Spot_manifest,
  savePath,
  centre = 1,
  broad = 1,
  spaceFile,
  Maskfile,
  imagefile,
  spot_r_min = 12,
  img_import = 1,
  spot_r_max = 20,
  Step = 10,
  diffusion_rate = 0.1,
  enrichment_score = TRUE,
  netfile,
  cluster_num = 50,
  geneenrichment = F,
  genelist = NULL
)

Arguments

SC_obj	You can also load RNA-seq use an existed Seruat object.
Spot_manifest	The TIST results returned by function "Meta_St_img_unsupervised"
savePath	The address where the results stored.
centre	The covariance matrix of distance Gaussian kernel, we default element in covariance matrix is identical.
broad	The mean of distance Gaussian kernel.
spaceFile	The address where the local file of all spots is stored. Such as "spatial/tissue_positions_list.csv".
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".
spot_r_min	A min window to select Image features. Default is 12.
img_import	The image feature weight for feature integration.
spot_r_max	A max window to select Image features. Default is 20.
Step	Control the step length of random walk for walkstrap method.
diffusion_rate	The diffusion rate, is related to temperature, liquid viscosity, and molecular size.
netfile	The TIST-net build by function "Meta_St_img_unsupervised"
cluster_num	The number of init cluster for image. Default is 50.
geneenrichment	Whether to perform gene enhancement analysis. Default True.
genelist	if geneenrichment is True, the analysis gene list.

Examples

    Diffusion_net_analysis(SC_obj=SC_obj,
    Spot_manifest = Spot_manifest_imgunsup,
    savePath= savePath,
    centre = 1,
    broad = 2,
    spaceFile=spaceFile,
    Maskfile=Maskfile,
    imagefile=imagefile,
    spot_r_min = 12,
    img_import = 1,
    spot_r_max = 20,
    Step = NULL,
    diffusion_rate = dd,
    netfile = netfile,
    geneenrichment = T,
    genelist = NULL)

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