

rsync -ruptl /home/rsat/packages/rsat-2021/rsat/perl-scripts/lib/js results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees


rsync -ruptl /home/rsat/packages/rsat-2021/rsat/public_html/images/program_icons/matrix-clustering_icons results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees


/home/rsat/packages/rsat-2021/rsat/perl-scripts/convert-matrix -i data/motifs/fungi/JASPAR_2022_UNVALIDATED_fungi.tf -from tf -to tf -o results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_data/JASPAR_2022_fungi_UNVALIDATED_input_motifs_processed_1.tf


/home/rsat/packages/rsat-2021/rsat/perl-scripts/convert-matrix -i results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_data/JASPAR_2022_fungi_UNVALIDATED_input_motifs_processed_1.tf -from tf -to transfac -prefix_id JASPAR_2022_fungi_UNVALIDATED -o results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_data/JASPAR_2022_fungi_UNVALIDATED_input_motifs_processed.tf


cat results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_data/JASPAR_2022_fungi_UNVALIDATED_input_motifs_processed.tf  > results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_data/input_motifs_processed.tf


/home/rsat/packages/rsat-2021/rsat/perl-scripts/convert-matrix -i results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_data/input_motifs_processed.tf -split -from tf -to tf -o results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_data/motif


 cat /home/rsat/packages/rsat-2021/rsat/R-scripts/matrix-clustering.R | /usr/bin/R --slave --no-save --no-restore --no-environ --args " infile = 'results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = 'results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = 'results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/distance_table.tab'; alignment.file = 'results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/alignment_table.tab'; verbosity = 1; metric = 'Ncor'; heatmap.color.palette = 'YlOrRd'; heatmap.color.classes = '9'; export.newick = 0; radial.only = 1; draw.heatmap = 0; draw.consensus = 0; pos.hclust.in.heatmap = 'column'; lthsp = 'cor_0.6_Ncor_0.4_'; out.prefix = 'results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED'; "


rsat convert-matrix -i results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/cluster_1_motif_IDs.tab -o results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_data/cluster_1_transfac_motifs.tf


rm -r results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_pairwise_compa_logos


/home/rsat/packages/rsat-2021/rsat/perl-scripts/text-to-html -i results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/pairwise_compa_matrix_descriptions.tab -o results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_html/pairwise_compa_matrix_descriptions.html


/home/rsat/packages/rsat-2021/rsat/perl-scripts/text-to-html -i results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/distance_table.tab -o results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/distance_table.html


/home/rsat/packages/rsat-2021/rsat/perl-scripts/text-to-html -i results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/alignment_table.tab -o results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/alignment_table.html


/home/rsat/packages/rsat-2021/rsat/perl-scripts/text-to-html -i results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/clusters.tab -o results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/clusters.html


/home/rsat/packages/rsat-2021/rsat/perl-scripts/text-to-html -i results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/clusters_motif_names.tab -o results/JASPAR_2022_matrix_clustering/fungi/UNVALIDATED/radial_trees/JASPAR_2022_matrix_clustering_fungi_UNVALIDATED_tables/clusters_motif_names.html
