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function_catelog.txt
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56 lines (56 loc) · 6.84 KB
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Utility/CellTrekhelper.r:RemoveCellNotInCellTrek = function(...)
Utility/CellTrekhelper.r:RemoveScRNANotInCellTrek = function(scRNA_obj, CellTrek_obj)
Utility/CellTrekhelper.r:AddAssayToCellTrek = function(celltrek_obj, scRNA, assay ='SCT')
Utility/Celltrek_preprocess.R:CheckSharedColumns = function(sn, ST)
Utility/Celltrek_preprocess.R:FixColumnToIntegar = function(obj, columns)
QC/qc_metrics.r:PlotDegreeDistribution = function(graph_obj)
Plot/function_CellTrek_Plot_helper.r:CellTrekPlot = function(data_df, group.by, coord_cols, pt_size = 1, label=T, label_size = 5, label_col = 'black')
Plot/function_CellTrek_Plot_helper.r:UmapCellTrekPlot = function(celltrek_obj, group.by, pt_size = 1, label=T, label_size = 5, label_col = 'black', filter_na = F)
Plot/function_CellTrek_Plot_helper.r:SpatialCellTrekPlot = function(celltrek_obj, group.by, pt_size = 1, label=T, label_size = 5, label_col = 'black', filter_na = F)
Plot/function_CellTrek_Plot_helper.r:CellTrekContour = function(obj, cell_column, cell_highlight, show_countour = T,
Palette/function_color.r:get_discrete_colors = function(n)
Heatmap/CellTrek_neighbor_cluster_heatmap.r:GetExpressionData = function(plot_obj, sc_obj, assay = 'SCT', cell_mode = c('target_cells','all'), gene_mode = c('Variable','DEG'), gene_use =NULL)
Heatmap/CellTrek_neighbor_cluster_heatmap.r:GetTopGeneMatrix = function(expr_matrix, n_gene = 100)
Heatmap/CellTrek_neighbor_cluster_heatmap.r:MakeClusterHeatmap = function(plot_obj, sc_obj, assay = 'SCT', limit_gene_show = T, n_gene_show = 100, gene_to_label,
Heatmap/CellTrek_neighbor_cluster_heatmap.r:GetClusterMarkers = function(scRNA, plot_obj, assay = 'SCT', p_cutoff = 0.05, fc_cutoff = 0.2)
Heatmap/CellTrek_neighbor_cluster_heatmap.r:GetTopDegPerGroup = function(plot_obj, top_n = 5)
NeighborhoodProfilePlot/function_CellTrek_neighbor.r:GetAllNeighbors = function(obj, obj_graph, quary_pt, n_order = 1, exclude_quary = T)
NeighborhoodProfilePlot/function_CellTrek_neighbor.r:GetNeighborByIdent = function(obj, obj_graph, group.by, idents, n_order = 1, exclude_self = T)
NeighborhoodProfilePlot/function_CellTrek_neighbor.r:MakeCellNeighborhoodRatioPlot = function(obj, obj_graph, n_order = 1, cell_column, celltype_plt, neighbor_celltype, exclude_self=T,
NeighborhoodProfilePlot/function_CellTrek_neighbor.r:GetDelaunayEdgeDistanceTable = function(graph, layout)
NeighborhoodProfilePlot/function_CellTrek_neighbor.r:TrimDelaunayGraph = function(graph, layout, max_distance = 500)
NeighborhoodProfilePlot/function_CellTrek_neighbor_profile.r:MakeNeighborProfilePlotV2 = function(plot_info_obj, title_sample = '', reorder_profile=T)
NeighborhoodProfilePlot/function_CellTrek_neighbor_profile.r:ReorderProfilePlotByCellRatio = function(p_profile)
NeighborhoodProfilePlot/function_CellTrek_neighbor_profile.r:GetConnectionTable = function(obj, graph_obj)
NeighborhoodProfilePlot/function_CellTrek_neighbor_profile.r:GetNeighborCellTypeTable = function(obj, graph_obj, cell_column)
NeighborhoodProfilePlot/function_CellTrek_neighbor_profile.r:ClusterAndReorderTable = function(neighbor_count_df, n_km=3, celltype_col = 'Neighbor_celltype')
NeighborhoodProfilePlot/function_CellTrek_neighbor_profile.r:MakeNeighborProfilePlot = function(neighbor_df, palette_use='', Origin_celltype = '', title_sample = '', palette_cluster = '')
NeighborhoodProfilePlot/function_CellTrek_neighbor_profile.r:GetHclustKmeansTable = function(mtx, n_km, cluster_method = c('kmeans','hclust'))
NeighborhoodProfilePlot/function_CellTrek_neighbor_profile.r:MakeClusterPalette = function(k, celltype='')
Analysis/function_CellTrek_coexpression.r:CoExpressionPlot = function(cc_result)
Analysis/function_CellTrek_coexpression.r:consensuscluster_multiple_cells = function(obj_celltrek, sample_name = 'sample_1', cell_types, cell_type_col = 'cell_type_Abbr', assay = 'RNA', root_path)
Analysis/function_CellTrek_neighbor_deg.r:FindNeighborMarkers = function(celltrek_obj, graph_obj, group.by, ident, n_order = 2, cell_count_cutoff = 50, p_cutoff = 0.05, Assay = 'RNA', return_as= c('both','markers_only'))
Analysis/function_CellTrek_neighbor_deg.r:FindNeighborMarkers = function(celltrek_obj, graph_obj, group.by, ident, n_order = 2, cell_count_cutoff = 50, p_cutoff = 0.05, Assay = 'RNA', return_as= c('all','markers_only'))
Analysis/function_CellTrek_neighbor_deg.r:SplitSpatialCellTrekPlot = function(celltrek_obj, feature, split.by, meta_table, plot_title, ...)
Analysis/function_CellTrek_neighbor_deg.r:MarkerSplitSpatialCellTrekPlot = function(celltrek_obj, marker_result_list, feature, split_cell_col = NULL, ...)
Analysis/function_CellTrek_neighbor_deg.r:MarkerBubblePlot = function(marker_result_list, palette='', fc_cutoff = 0.5, p_cutoff = 0.05, max.overlaps = 10, expand_x_multi = 0.2)
Graph/function_CellTrek_graph_edge.r:GetEdgeCellTypeTable = function(plot_info_obj, cell_group = c('Tumor'), others_name = 'TME')
Graph/function_CellTrek_graph_edge.r:AddEdgeGroup = function(plot_info_obj, cell_group = c('Tumor'), others_name = 'TME')
Graph/function_CellTrek_graph_edge.r:GetEdgeInteractionType = function(edge_celltype_table, cell_group = c('Tumor'), others_name = 'TME')
Graph/function_CellTrek_graph_edge.r:EdgePlotByCell = function(plot_info_obj, color_edge_by = c('cell1','cell2'), segment_size= 0.5, title_size=20, plt_title = '',
Graph/function_CellTrek_MakePlotObject.R:PrepareSpatialPlotObject = function(obj, plt_graph, cell_column,
Graph/function_CellTrek_MakePlotObject.R:MakeSpatialTableList = function(obj, plt_graph, cell_column, cell_plot, flip_x = F, flip_y = T,
Graph/function_CellTrek_MakePlotObject.R:GetSpatialPaletteList = function(table_list, palette='', palette_cluster='')
Graph/function_CellTrek_MakePlotObject.R:MakeDelaunayGraphPlot = function(plot_info_obj, sample_name,
Graph/function_CellTrek_MakePlotObject.R:AddClusterHighlight = function(p_st, plot_info_obj, pt_size = 2.5, stroke = 0.2, remove_neighbor_cells = T)
Graph/function_CellTrek_MakePlotObject.R:AddDistanceToPoint = function(p_st, plot_info_obj ,center_pt = c(0,0),
Graph/function_CellTrek_MakePlotObject.R:SplitMetaByIdList = function(meta, list_of_ids)
Graph/function_CellTrek_MakePlotObject.R:GetCoordToPointDistance = function(coord_df, target_point = c(0,0), x_column = 'coord_x', y_column = 'coord_y')
Graph/function_CellTrek_MakePlotObject.R:DistanceBoxPlot = function(coord_target_df, group.by )
CNV/function_infercnv.r:GetInferCNVSubcluster = function(infercnv_obj)
CNV/function_infercnv.r:setRownames = function(df, rownames)
CNV/function_infercnv.r:bind_cols_dfs = function(df1, df2)
CCI/CCI_RL_interaction.r:GetReceptorLigandDistScoreTable = function(celltrek_obj, plot_info_obj, receptor, ligand)
CCI/CCI_RL_interaction.r:GetInteractionScores = function(RLscore_table, group.by = c('group','celltype'))
CCI/CCI_RL_interaction.r:GetRLscores = function(celltrek_obj, plot_info_obj, receptor, ligand)
CCI/CCI_RL_interaction.r:MakeCellTrekRLscore = function(plot_obj, pair_name = NA, direction = c('C1C2','C2C1'))