| 7 | 8 |
new file mode 100644 |
| ... | ... |
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| 1 |
+#' Combines all other package functions for one-step cell line comparison |
|
| 2 |
+#' @export |
|
| 3 |
+#' @param pathwayid A KEGG pathway ID of the form "hsa12345" |
|
| 4 |
+#' (only human pathways currently) |
|
| 5 |
+#' @param cell_line1 Choose from the set of cell lines: |
|
| 6 |
+#' (A375,A549,ASC,HA1E,HCC515,HEK293T,HEKTE,HEPG2,HT29,MCF7,NCIH716,NPC,PC3, |
|
| 7 |
+#' SHSY5Y,SKL,SW480,VCAP) |
|
| 8 |
+#' @param cell_line2 A cell line such that cell_line1 != cell_line2 |
|
| 9 |
+#' @param refine_by_cell_line A logical indicator |
|
| 10 |
+#' @param add_L1000_edge_data A logical indicator |
|
| 11 |
+#' @param data_type Choose from data types: (100_full, 100_bing, 50_lm) |
|
| 12 |
+#' @param pert_time Choose from (6,24,48,96,120,144,168) |
|
| 13 |
+#' @param only_mapped A logical indicator; if set to FALSE will return 'de-novo' |
|
| 14 |
+#' edges that 'exist' in data but are not documented in KEGG |
|
| 15 |
+#' @param significance_markup A logical indicator; if set to TRUE will color |
|
| 16 |
+#' edges based on direction and significance of correlation (as determined by |
|
| 17 |
+#' user-data-analysis) |
|
| 18 |
+#' @param layered_nodes A logical indicator; if set to TRUE will create a graph |
|
| 19 |
+#' with 'stacked' nodes that the user can manipulate when multiple nodes are |
|
| 20 |
+#' mapped to one location |
|
| 21 |
+#' @param graph_title An optional user-specified graph title |
|
| 22 |
+#' @param get_data A logical indicator; if set to true, will return the |
|
| 23 |
+#' 'expanded' edge information for the specified pathway |
|
| 24 |
+#' @param convert_KEGG_IDs A logical indicator; if set to TRUE KEGG |
|
| 25 |
+#' compounds will remain labeled via KEGG codes (do not need KEGGREST) |
|
| 26 |
+#' @return A dynamic map in Cytoscape automatically formatted for convenient |
|
| 27 |
+#' viewing and, if idicated by user, a data.frame object with detailed |
|
| 28 |
+#' information for 'expanded' KEGG edges |
|
| 29 |
+#' @examples \dontrun{
|
|
| 30 |
+#' |
|
| 31 |
+#' # Compare p53 pathway between cell lines A375 and A549: |
|
| 32 |
+#' KL_compare("hsa04115", "A375", "A549")
|
|
| 33 |
+#'} |
|
| 34 |
+ |
|
| 35 |
+KL_compare <- |
|
| 36 |
+ function(pathwayid, cell_line1 = NA, cell_line2 = NA, |
|
| 37 |
+ refine_by_cell_line = TRUE, |
|
| 38 |
+ add_L1000_edge_data = TRUE, |
|
| 39 |
+ significance_markup = TRUE, |
|
| 40 |
+ data_type = "100_full", |
|
| 41 |
+ pert_time = 96, |
|
| 42 |
+ only_mapped = TRUE, |
|
| 43 |
+ get_data = FALSE, |
|
| 44 |
+ convert_KEGG_IDs = TRUE, |
|
| 45 |
+ graph_title = "default", |
|
| 46 |
+ tidy_edges = TRUE, |
|
| 47 |
+ layered_nodes = FALSE){
|
|
| 48 |
+ cell_lines <- c("A375","A549","ASC","HA1E","HCC515","HEK293T","HEKTE",
|
|
| 49 |
+ "HEPG2","HT29","MCF7","NCIH716","NPC","PC3","SHSY5Y", |
|
| 50 |
+ "SKL","SW480","VCAP") |
|
| 51 |
+ if (is.na(cell_line1)){
|
|
| 52 |
+ warning(paste0( |
|
| 53 |
+ 'Please choose one of the following for cell_line1: ', |
|
| 54 |
+ cell_lines)) |
|
| 55 |
+ return() |
|
| 56 |
+ } |
|
| 57 |
+ if (is.na(cell_line2)){
|
|
| 58 |
+ warning(paste0('Please choose one the following for cell_line2: ',
|
|
| 59 |
+ list(cell_lines[cell_lines != cell_line1]))) |
|
| 60 |
+ return() |
|
| 61 |
+ } |
|
| 62 |
+ |
|
| 63 |
+ if (cell_line2 == cell_line1){
|
|
| 64 |
+ warning(paste0('cell_line1 = cell_line2; ',
|
|
| 65 |
+ 'please choose from the following for cell_line2: ', |
|
| 66 |
+ list(cell_lines[cell_lines != cell_line1]))) |
|
| 67 |
+ return() |
|
| 68 |
+ } |
|
| 69 |
+ |
|
| 70 |
+ KGML <- get_KGML(pathwayid, get_if_no_edges = TRUE) |
|
| 71 |
+ if(!isS4(KGML)){
|
|
| 72 |
+ return() |
|
| 73 |
+ } |
|
| 74 |
+ KEGG_mappings <- |
|
| 75 |
+ expand_KEGG_mappings(KGML,convert_KEGG_IDs = convert_KEGG_IDs) |
|
| 76 |
+ if (refine_by_cell_line) {
|
|
| 77 |
+ full_mappings1 <- KEGG_mappings |
|
| 78 |
+ KEGG_mappings1 <- refine_mappings(KEGG_mappings, cell_line1) |
|
| 79 |
+ for (i in 1:nrow(full_mappings1)){
|
|
| 80 |
+ if(!full_mappings1$entryID[i] %in% KEGG_mappings$entryID){
|
|
| 81 |
+ full_mappings1$BGcolor[i] <- "#d3d3d3" |
|
| 82 |
+ full_mappings1$in_relationship <- 0 |
|
| 83 |
+ } |
|
| 84 |
+ } |
|
| 85 |
+ full_mappings2 <- KEGG_mappings |
|
| 86 |
+ KEGG_mappings2 <- refine_mappings(KEGG_mappings, cell_line2) |
|
| 87 |
+ for (i in 1:nrow(full_mappings2)){
|
|
| 88 |
+ if(!full_mappings2$entryID[i] %in% KEGG_mappings$entryID){
|
|
| 89 |
+ full_mappings2$BGcolor[i] <- "#d3d3d3" |
|
| 90 |
+ full_mappings2$in_relationship <- 0 |
|
| 91 |
+ } |
|
| 92 |
+ } |
|
| 93 |
+ } |
|
| 94 |
+ expanded_edges <- expand_KEGG_edges(KGML, KEGG_mappings) |
|
| 95 |
+ if(expanded_edges$type[1] == "dummy"){
|
|
| 96 |
+ graph_title <- paste0("Pathway = ", pathwayid, ":",
|
|
| 97 |
+ KGML@pathwayInfo@title, |
|
| 98 |
+ "Cell-Line: ", cell_line, |
|
| 99 |
+ " *No Edges in Pathway") |
|
| 100 |
+ } |
|
| 101 |
+ |
|
| 102 |
+ if (nrow(expanded_edges[expanded_edges$type == "maplink",]) == |
|
| 103 |
+ nrow(expanded_edges) & only_mapped) {
|
|
| 104 |
+ edge_map <- edge_mapping_info(expanded_edges) |
|
| 105 |
+ if (graph_title == "default"){
|
|
| 106 |
+ graph_title <- paste0("Pathway = ", pathwayid, ":",
|
|
| 107 |
+ KGML@pathwayInfo@title, "Cell-Line: ", |
|
| 108 |
+ cell_line, " *No Edges in Data") |
|
| 109 |
+ } |
|
| 110 |
+ warning("All documented edges are of type 'maplink';
|
|
| 111 |
+ Overlap data cannot be mapped to selected pathway") |
|
| 112 |
+ } |
|
| 113 |
+ cell_data1 <- overlap_info(KGML, KEGG_mappings, cell_line1, |
|
| 114 |
+ data_type = data_type, |
|
| 115 |
+ pert_time = pert_time) |
|
| 116 |
+ |
|
| 117 |
+ cell_data2 <- overlap_info(KGML, KEGG_mappings, cell_line2, |
|
| 118 |
+ data_type = data_type, |
|
| 119 |
+ pert_time = pert_time) |
|
| 120 |
+ |
|
| 121 |
+ for (i in 1:nrow(cell_data1)){
|
|
| 122 |
+ UP <- cell_data1$UP[i] + 0.5 |
|
| 123 |
+ DOWN <- cell_data1$DOWN[i] + 0.5 |
|
| 124 |
+ UK1_DK2 <- cell_data1$UK1_DK2[i] + 0.5 |
|
| 125 |
+ DK1_UK2 <- cell_data1$DK1_UK2[i] + 0.5 |
|
| 126 |
+ cell_data1$OR_1[i] <- (UP*DOWN)/(UK1_DK2*DK1_UK2) |
|
| 127 |
+ cell_data1$SE_1[i] <-sqrt(1/UP + 1/DOWN + 1/UK1_DK2 + 1/DK1_UK2) |
|
| 128 |
+ cell_data1$log_OR_1[i] <- log(cell_data1$OR_1[i]) |
|
| 129 |
+ } |
|
| 130 |
+ |
|
| 131 |
+ for (i in 1:nrow(cell_data2)){
|
|
| 132 |
+ UP <- cell_data2$UP[i] + 0.5 |
|
| 133 |
+ DOWN <- cell_data2$DOWN[i] + 0.5 |
|
| 134 |
+ UK1_DK2 <- cell_data2$UK1_DK2[i] + 0.5 |
|
| 135 |
+ DK1_UK2 <- cell_data2$DK1_UK2[i] + 0.5 |
|
| 136 |
+ cell_data2$OR_2[i] <- (UP*DOWN)/(UK1_DK2*DK1_UK2) |
|
| 137 |
+ cell_data2$SE_2[i] <-sqrt(1/UP + 1/DOWN + 1/UK1_DK2 + 1/DK1_UK2) |
|
| 138 |
+ cell_data2$log_OR_2[i] <- log(cell_data2$OR_2[i]) |
|
| 139 |
+ } |
|
| 140 |
+ |
|
| 141 |
+ if (!is.na(cell_data1)[1,1] & !is.na(cell_data2)[1,1]) {
|
|
| 142 |
+ edges_plus_data1 <- add_edge_data(expanded_edges, KEGG_mappings, |
|
| 143 |
+ cell_data1, c(15,16), |
|
| 144 |
+ only_mapped = only_mapped) |
|
| 145 |
+ edges_plus_data2 <- add_edge_data(expanded_edges, KEGG_mappings, |
|
| 146 |
+ cell_data2, c(15,16), |
|
| 147 |
+ only_mapped = only_mapped) |
|
| 148 |
+ edges_plus_data1$unique_ID <- paste0(edges_plus_data1$entry1symbol, ":", edges_plus_data1$entry2symbol, ":", edges_plus_data1$edgeID) |
|
| 149 |
+ edges_plus_data2$unique_ID <- paste0(edges_plus_data2$entry1symbol, ":", edges_plus_data2$entry2symbol, ":", edges_plus_data2$edgeID) |
|
| 150 |
+ |
|
| 151 |
+ edges_compare <- merge(edges_plus_data1, edges_plus_data2[,c(18,19,21)], by = "unique_ID") |
|
| 152 |
+ |
|
| 153 |
+ for(i in 1:nrow(edges_compare)){
|
|
| 154 |
+ if (!is.na(edges_compare$log_OR_1[i]) & !is.na(edges_compare$log_OR_2[i])){
|
|
| 155 |
+ edges_compare$test[i] <- (edges_compare$log_OR_1[i] - edges_compare$log_OR_2[i])/ |
|
| 156 |
+ sqrt(edges_compare$SE_1[i]^2 + edges_compare$SE_2[i]^2) |
|
| 157 |
+ edges_compare$summary_score[i] <- exp(abs(edges_compare$test[i])) |
|
| 158 |
+ |
|
| 159 |
+ |
|
| 160 |
+ if (edges_compare$test[i] <= qnorm(0.1) | edges_compare$test[i] >= qnorm(0.9)){
|
|
| 161 |
+ edges_compare$significant[i] <- 1 |
|
| 162 |
+ } |
|
| 163 |
+ else {
|
|
| 164 |
+ edges_compare$significant[i] <- 0 |
|
| 165 |
+ } |
|
| 166 |
+ } |
|
| 167 |
+ else {
|
|
| 168 |
+ edges_compare$test[i] <- NA |
|
| 169 |
+ edges_compare$summary_score[i] <- 0 |
|
| 170 |
+ edges_compare$significant[i] <- NA |
|
| 171 |
+ } |
|
| 172 |
+ } |
|
| 173 |
+ |
|
| 174 |
+ edge_map <- edge_mapping_info(edges_compare, data_added = TRUE) |
|
| 175 |
+ for (i in 1:nrow(edge_map)){
|
|
| 176 |
+ if (is.na(edge_map$test[i])){
|
|
| 177 |
+ edge_map$has_data[i] <- 0 |
|
| 178 |
+ edge_map$color[i] <- "#808080" |
|
| 179 |
+ } |
|
| 180 |
+ } |
|
| 181 |
+ if ("premapped" %in% names (edge_map)) {
|
|
| 182 |
+ premapped <- edge_map$premapped |
|
| 183 |
+ drop <- "premapped" |
|
| 184 |
+ edge_map <- edge_map[, ! names(edge_map) %in% drop] |
|
| 185 |
+ edge_map$premapped <- premapped |
|
| 186 |
+ } |
|
| 187 |
+ for (i in 1:nrow(edge_map)){
|
|
| 188 |
+ if (!is.na(edge_map$log_OR_1[i]) & |
|
| 189 |
+ !is.na(edge_map$log_OR_2[i])){
|
|
| 190 |
+ if (edge_map$test[i] < 0){
|
|
| 191 |
+ if (edge_map$significant[i] == 0){
|
|
| 192 |
+ edge_map$color[i] <- "#82E0AA" |
|
| 193 |
+ } |
|
| 194 |
+ if (edge_map$significant[i] == 1){
|
|
| 195 |
+ edge_map$color[i] <- "#1E8449" |
|
| 196 |
+ } |
|
| 197 |
+ } |
|
| 198 |
+ if (edge_map$test[i] > 0){
|
|
| 199 |
+ if (edge_map$significant[i] == 0){
|
|
| 200 |
+ edge_map$color[i] <- "#E67E22" |
|
| 201 |
+ } |
|
| 202 |
+ if (edge_map$significant[i] == 1){
|
|
| 203 |
+ edge_map$color[i] <- "#BA4A00" |
|
| 204 |
+ } |
|
| 205 |
+ } |
|
| 206 |
+ } |
|
| 207 |
+ } |
|
| 208 |
+ if (tidy_edges == TRUE) {
|
|
| 209 |
+ edge_IDs <- seq(min(edge_map$edgeID), max(edge_map$edgeID)) |
|
| 210 |
+ for (i in edge_IDs){
|
|
| 211 |
+ edge_map <- tidy_edge(edges = edge_map, |
|
| 212 |
+ edge_id = edge_IDs[i], |
|
| 213 |
+ by_significance = TRUE) |
|
| 214 |
+ } |
|
| 215 |
+ } |
|
| 216 |
+ |
|
| 217 |
+ if (graph_title == "default"){
|
|
| 218 |
+ graph_title <- paste0("Pathway = ", pathwayid, ":",
|
|
| 219 |
+ KGML@pathwayInfo@title, " - ", |
|
| 220 |
+ cell_line1 ,"vs", cell_line2, ", |
|
| 221 |
+ Data type: ", data_type) |
|
| 222 |
+ } |
|
| 223 |
+ } |
|
| 224 |
+ |
|
| 225 |
+ node_map <- node_mapping_info(KEGG_mappings) |
|
| 226 |
+ |
|
| 227 |
+ graph_object <- get_graph_object(node_map, edge_map, |
|
| 228 |
+ layered_nodes = layered_nodes) |
|
| 229 |
+ |
|
| 230 |
+ edge_width_attribute = "summary_score" |
|
| 231 |
+ |
|
| 232 |
+ if (edge_width_attribute %in% names(igraph::edge_attr(graph_object))){
|
|
| 233 |
+ min.summary_score <- min(abs(igraph::E(graph_object)$summary_score), |
|
| 234 |
+ na.rm = TRUE) |
|
| 235 |
+ max.summary_score <- max(abs(igraph::E(graph_object)$summary_score), |
|
| 236 |
+ na.rm = TRUE) |
|
| 237 |
+ map_edge_width <- TRUE |
|
| 238 |
+ } |
|
| 239 |
+ |
|
| 240 |
+ cyto_vis(graph_object, title = graph_title, |
|
| 241 |
+ edge_width_attribute = "summary_score") |
|
| 242 |
+ if(get_data){
|
|
| 243 |
+ return(edge_map) |
|
| 244 |
+ } |
|
| 245 |
+ } |
| 0 | 246 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,64 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/KL_compare.R |
|
| 3 |
+\name{KL_compare}
|
|
| 4 |
+\alias{KL_compare}
|
|
| 5 |
+\title{Combines all other package functions for one-step cell line comparison}
|
|
| 6 |
+\usage{
|
|
| 7 |
+KL_compare(pathwayid, cell_line1 = NA, cell_line2 = NA, |
|
| 8 |
+ refine_by_cell_line = TRUE, add_L1000_edge_data = TRUE, |
|
| 9 |
+ significance_markup = TRUE, data_type = "100_full", pert_time = 96, |
|
| 10 |
+ only_mapped = TRUE, get_data = FALSE, convert_KEGG_IDs = TRUE, |
|
| 11 |
+ graph_title = "default", tidy_edges = TRUE, layered_nodes = FALSE) |
|
| 12 |
+} |
|
| 13 |
+\arguments{
|
|
| 14 |
+\item{pathwayid}{A KEGG pathway ID of the form "hsa12345"
|
|
| 15 |
+(only human pathways currently)} |
|
| 16 |
+ |
|
| 17 |
+\item{cell_line1}{Choose from the set of cell lines:
|
|
| 18 |
+(A375,A549,ASC,HA1E,HCC515,HEK293T,HEKTE,HEPG2,HT29,MCF7,NCIH716,NPC,PC3, |
|
| 19 |
+SHSY5Y,SKL,SW480,VCAP)} |
|
| 20 |
+ |
|
| 21 |
+\item{cell_line2}{A cell line such that cell_line1 != cell_line2}
|
|
| 22 |
+ |
|
| 23 |
+\item{refine_by_cell_line}{A logical indicator}
|
|
| 24 |
+ |
|
| 25 |
+\item{add_L1000_edge_data}{A logical indicator}
|
|
| 26 |
+ |
|
| 27 |
+\item{significance_markup}{A logical indicator; if set to TRUE will color
|
|
| 28 |
+edges based on direction and significance of correlation (as determined by |
|
| 29 |
+user-data-analysis)} |
|
| 30 |
+ |
|
| 31 |
+\item{data_type}{Choose from data types: (100_full, 100_bing, 50_lm)}
|
|
| 32 |
+ |
|
| 33 |
+\item{pert_time}{Choose from (6,24,48,96,120,144,168)}
|
|
| 34 |
+ |
|
| 35 |
+\item{only_mapped}{A logical indicator; if set to FALSE will return 'de-novo'
|
|
| 36 |
+edges that 'exist' in data but are not documented in KEGG} |
|
| 37 |
+ |
|
| 38 |
+\item{get_data}{A logical indicator; if set to true, will return the
|
|
| 39 |
+'expanded' edge information for the specified pathway} |
|
| 40 |
+ |
|
| 41 |
+\item{convert_KEGG_IDs}{A logical indicator; if set to TRUE KEGG
|
|
| 42 |
+compounds will remain labeled via KEGG codes (do not need KEGGREST)} |
|
| 43 |
+ |
|
| 44 |
+\item{graph_title}{An optional user-specified graph title}
|
|
| 45 |
+ |
|
| 46 |
+\item{layered_nodes}{A logical indicator; if set to TRUE will create a graph
|
|
| 47 |
+with 'stacked' nodes that the user can manipulate when multiple nodes are |
|
| 48 |
+mapped to one location} |
|
| 49 |
+} |
|
| 50 |
+\value{
|
|
| 51 |
+A dynamic map in Cytoscape automatically formatted for convenient |
|
| 52 |
+viewing and, if idicated by user, a data.frame object with detailed |
|
| 53 |
+information for 'expanded' KEGG edges |
|
| 54 |
+} |
|
| 55 |
+\description{
|
|
| 56 |
+Combines all other package functions for one-step cell line comparison |
|
| 57 |
+} |
|
| 58 |
+\examples{
|
|
| 59 |
+\dontrun{
|
|
| 60 |
+ |
|
| 61 |
+# Compare p53 pathway between cell lines A375 and A549: |
|
| 62 |
+KL_compare("hsa04115", "A375", "A549")
|
|
| 63 |
+} |
|
| 64 |
+} |
