Description Usage Arguments Value
A master function to perform the full workflow of ClusterMap.
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)
|
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. |
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.
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