cluster_map: cluster_map

Description Usage Arguments Value

View source: R/master.R

Description

A master function to perform the full workflow of ClusterMap.

Usage

1
2
3
cluster_map(marker_file_list, edge_cutoff = 0.1, output,
  cell_num_list = NULL, single_obj_list = NULL, comb_obj = NULL,
  comb_delim = "-", k = 5)

Arguments

marker_file_list

A list of csv files with names. Each file is a marker gene table for a sample. The columns named as 'cluster' and 'gene' are required.

edge_cutoff

The edge length cutoff to decide the sub-nodes to merge or not. DEFAULT is 0.1.

output

The output directory to save the matching results.

cell_num_list

A list of vector of cell numbers for each group and each sample.

single_obj_list

A list of Seurat object for each sample, with the same list names as the list names of marker_file_list.

comb_obj

A Seurat object for the combined sample. Cells in different samples are labelled by the sample names with the comb_delim. The sample names should be the same as the list names of marker_file_list.

comb_delim

The delimiter used in the cell names in the combined object to connect sample name and cell name in individual sample. DEFAULT is '-'.

k

K-nearest neighbours used to calculate distance. DEFAULT is 5.

Value

A dataframe of the matching results. Heatmap of marker genes, the corresponding dendrogram, circos plot and recolored t-SNE plots will be saved into files.


xgaoo/ClusterMap documentation built on Oct. 9, 2021, 5:31 a.m.