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Mainly spacing and replacing = with =
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,74 +1,66 @@ | ||
| entitieSelection=function(data, | ||
| type, | ||
| TopK2Show=NA, | ||
| additionalInput_row_anno=NA, | ||
| additionalInput_row_anno_factor=NA, | ||
| additionalInput_sample_annotation_types=NA, | ||
| additionalInput_ctrl_idx=NA, | ||
| additionalInput_cmp_idx=NA, | ||
| psig_threhsold=NA){ | ||
| entitieSelection <- function( | ||
| data, | ||
| type, | ||
| TopK2Show=NA, | ||
| additionalInput_row_anno=NA, | ||
| additionalInput_row_anno_factor=NA, | ||
| additionalInput_sample_annotation_types=NA, | ||
| additionalInput_ctrl_idx=NA, | ||
| additionalInput_cmp_idx=NA, | ||
| psig_threhsold=NA | ||
| ){ | ||
| # to cover: c("TopK","significant_LFC","LFC_onlySig","rowAnno_based") | ||
| filtered_data=assay(data) | ||
| orderMakesSense_flag=FALSE | ||
| filtered_data <- assay(data) | ||
| orderMakesSense_flag <- FALSE | ||
| print("Entitie Selection") | ||
| #print(additionalInput_row_anno) | ||
| if(any(type=="rowAnno_based") & !(any(is.na(additionalInput_row_anno) &is.na(additionalInput_row_anno_factor))) & !any(additionalInput_row_anno_factor=="all")){ | ||
| # Note here this only what to show, LFCs and more importantly multiple test correction will be done on the entire set (without the row anno based selection!!) | ||
| if(any(additionalInput_row_anno_factor=="all")){ | ||
| filtered_data = filtered_data | ||
| }else{ | ||
| filtered_data = filtered_data[which(data$annotation_rows[,additionalInput_row_anno] %in% additionalInput_row_anno_factor),] | ||
| filtered_data <- filtered_data | ||
| } else{ | ||
| filtered_data <- filtered_data[which(data$annotation_rows[, additionalInput_row_anno] %in% additionalInput_row_anno_factor),] | ||
| } | ||
| } | ||
| if(!(is.na(additionalInput_sample_annotation_types)) & !(is.na(additionalInput_ctrl_idx)) & !(is.na(additionalInput_cmp_idx))){ | ||
| if(any(type=="significant_LFC")){ | ||
| # sort based on significance | ||
| # need LFCs | ||
| # is reachable from here? selectedData_processed()[[input$omicType]]$sample_table | ||
| # sort based on significance need LFCs | ||
| ctrl_samples_idx <- which(colData(data)[,additionalInput_sample_annotation_types]%in%additionalInput_ctrl_idx) | ||
| comparison_samples_idx <- which(colData(data)[,additionalInput_sample_annotation_types]%in%additionalInput_cmp_idx) | ||
| if((length(ctrl_samples_idx) <= 1) | (length(comparison_samples_idx) <= 1)){ | ||
| warning("LFC makes no sense just having a single sample per conidition, which is here the case!") | ||
| filtered_data=NULL | ||
| }else{ | ||
| LFC_output=getLFC(filtered_data,ctrl_samples_idx,comparison_samples_idx) | ||
| filtered_data=filtered_data[rownames(LFC_output)[order(LFC_output$p_adj,decreasing = F)],,drop=F] | ||
| orderMakesSense_flag=T | ||
| filtered_data <- NULL | ||
| } else{ | ||
| LFC_output <- getLFC(filtered_data, ctrl_samples_idx, comparison_samples_idx) | ||
| filtered_data <- filtered_data[rownames(LFC_output)[order(LFC_output$p_adj, decreasing = F)],, drop=F] | ||
| orderMakesSense_flag <- T | ||
| } | ||
|
|
||
| } | ||
| if(any(type=="LFC_onlySig")){ | ||
| ctrl_samples_idx<-which(colData(data)[,additionalInput_sample_annotation_types]%in%additionalInput_ctrl_idx) | ||
| comparison_samples_idx<-which(colData(data)[,additionalInput_sample_annotation_types]%in%additionalInput_cmp_idx) | ||
| LFC_output=getLFC(filtered_data,ctrl_samples_idx,comparison_samples_idx) | ||
| LFC_output <- getLFC(filtered_data, ctrl_samples_idx, comparison_samples_idx) | ||
| if(!(any(LFC_output$p_adj<psig_threhsold))){ | ||
| warning("No single entry left! Maybe adjust psig_threhsold_heatmap (but do not put it arbitraly high!)") | ||
| #req(FALSE) -> can we speak from here to output$debug? | ||
| filtered_data=NULL | ||
| }else{ | ||
| filtered_data=filtered_data[rownames(LFC_output)[which(LFC_output$p_adj<psig_threhsold)],,drop=F] | ||
| filtered_data=filtered_data[rownames(LFC_output)[order(LFC_output$LFC,decreasing = F)],,drop=F] | ||
| orderMakesSense_flag=T | ||
| filtered_data <- NULL | ||
| } else{ | ||
| filtered_data <- filtered_data[rownames(LFC_output)[which(LFC_output$p_adj<psig_threhsold)],, drop=F] | ||
| filtered_data <- filtered_data[rownames(LFC_output)[order(LFC_output$LFC, decreasing = F)],, drop=F] | ||
| orderMakesSense_flag <- T | ||
| } | ||
|
|
||
| } | ||
| } | ||
|
|
||
| if(any(type=="TopK")){ | ||
| if(orderMakesSense_flag){ | ||
| #assumes the data to be sorted somehow | ||
| if(nrow(filtered_data)>TopK2Show){ | ||
| filtered_data=filtered_data[c(1:TopK2Show),,drop=F] | ||
| }else{ | ||
| filtered_data=filtered_data | ||
| filtered_data <- filtered_data[c(1:TopK2Show),, drop=F] | ||
| } else{ | ||
| filtered_data <- filtered_data | ||
| } | ||
| }else{ | ||
| filtered_data=NULL | ||
| } else{ | ||
| filtered_data <- NULL | ||
| } | ||
|
|
||
| } | ||
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| return(filtered_data) | ||
| } |