# high confidence: as seen from the table (bold italics), 7% of # simulated samples reach
threshold 2 for at least 10 voxels
# set the minimum score:
h_thres¼ 2
# and minimum number of mapped voxels:
h_thres_num¼ 10# medium confidence values (marked in the table in bold):
m_thres¼-1
m_thres_num¼ 10# low confidence values (marked in the table in italics):
l_thres¼-2
l_thres_num¼ 15- Using these values, we now summarize the results for
sequenced cells:
results <- summary_results(results_scores,h_thres,m_thres,l_thres,h_thres_num,
m_thres_num,l_thres_num)- In this final step, summary output table will be generated,
containing the number of voxels that passed the threshold for
each sequenced cell, and the mapping confidence level.
3.4 Visualization 1. We can visualize the reference datapoints and the voxels therein
that correspond to the single cells according to the mapping
results, using the mapping visualization tool at:http://www.
ebi.ac.uk/~jbpettit/map_viewer/(based onBioWeb3D[9]).
- For importing toBioweb3D, the mapping results need to be
scaled:
scaled_results<-scale_res(results_scores,h_thres,m_thres,l_thres,h_thres_num,
m_thres_num,l_thres_num,rownames(rna_seq))
write.table(file¼"scaled_results.csv",sep¼",",scaled_results,row.names¼FALSE,
quote¼FALSE)- For visualization, import the3D_coordinates_atlastable
as the main dataset andscaled_resultstable as cluster data.
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