creates Giotto object directly from a 10X visium folder
原始数据文件夹子
1## provide path to visium folder
dir.create( “G:/silicosis/sicosis/gitto/silicosis_data/”)
data_path = “G:/silicosis/sicosis/gitto/silicosis_data/”
visium_brain = createGiottoVisiumObject(visium_dir = data_path,
-
h5_visium_path = "G:/raw_material for omics_chaojie/silicosis for spatial transcription/B26/2.3.h5_files/filtered_feature_bc_matrix.h5", -
h5_gene_ids = c("symbols"), -
h5_image_png_path= "G:/raw_material for omics_chaojie/silicosis for spatial transcription/B26/spatial/tissue_lowres_image.png", -
h5_tissue_positions_path = "G:/raw_material for omics_chaojie/silicosis for spatial transcription/B26/spatial/tissue_positions_list.csv", -
instructions = instrs)
A path to an .h5 10X file was provided and will be used
Consider to install these (optional) packages to run all possible Giotto commands for spatial analyses: smfishHmrf trendsceek SPARK multinet RTriangle FactoMiner
Giotto does not automatically install all these packages as they are not absolutely required and this reduces the number of dependencies
createGiottoVisiumObject(
visium_dir = NULL,
expr_data = c(“raw”, “filter”),
gene_column_index = 1,
h5_visium_path = NULL,
h5_gene_ids = c(“symbols”, “ensembl”),
h5_tissue_positions_path = NULL,
h5_image_png_path = NULL,
png_name = NULL,
xmax_adj = 0,
xmin_adj = 0,
ymax_adj = 0,
ymin_adj = 0,
instructions = NULL,
cores = NA,
verbose = TRUE
)
Arguments
visium_dir
path to the 10X visium directory [required]
expr_data
raw or filtered data (see details)
gene_column_index
which column index to select (see details)
h5_visium_path
path to visium 10X .h5 file
h5_gene_ids
gene names as symbols (default) or ensemble gene ids
h5_tissue_positions_path
path to tissue locations (.csv file)
h5_image_png_path
path to tissue .png file (optional)
png_name
select name of png to use (see details)
xmax_adj
adjustment of the maximum x-value to align the image
xmin_adj
adjustment of the minimum x-value to align the image
ymax_adj
adjustment of the maximum y-value to align the image
ymin_adj
adjustment of the minimum y-value to align the image
instructions
list of instructions or output result from createGiottoInstructions
cores
how many cores or threads to use to read data if paths are provided
verbose
be verbose
Value
giotto object
Details
If starting from a Visium 10X directory:
expr_data: raw will take expression data from raw_feature_bc_matrix and filter from filtered_feature_bc_matrix
gene_column_index: which gene identifiers (names) to use if there are multiple columns (e.g. ensemble and gene symbol)
png_name: by default the first png will be selected, provide the png name to override this (e.g. myimage.png)
If starting from a Visium 10X .h5 file
h5_visium_path: full path to .h5 file: /your/path/to/visium_file.h5
h5_tissue_positions_path: full path to spatial locations file: /you/path/to/tissue_positions_list.csv
h5_image_png_path: full path to png: /your/path/to/images/tissue_lowres_image.png