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Tanushree Tunstall 2022-09-09 20:25:09 +01:00
parent f9db5cbc33
commit 27f70afb2c
2 changed files with 350 additions and 325 deletions
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35
drug-target/server.R
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@ -124,9 +124,18 @@ function(input, output, session) {
# different data ranges required for SNP distances # different data ranges required for SNP distances
snp_ligand_dist_df3 = merged_df3[merged_df3$ligand_distance<input$snp_ligand_dist,] snp_ligand_dist_df3 = merged_df3[merged_df3[['ligand_distance']]<input$snp_ligand_dist,]
snp_interface_dist_df3 = merged_df3[merged_df3$interface_dist<input$snp_interface_dist,] if ("interface_dist" %in% colnames(merged_df3)){
snp_nca_dist_df3 = merged_df3[merged_df3$nca_distance<input$snp_nca_dist,] snp_interface_dist_df3 = merged_df3[merged_df3[['interface_dist']]<input$snp_interface_dist,]
} else {
snp_interface_dist_df3 = NULL
}
if ("nca_distance" %in% colnames(merged_df3)){
snp_nca_dist_df3 = merged_df3[merged_df3[['nca_distance']]<input$snp_nca_dist,]
} else {
snp_nca_dist_df3 = NULL
}
stability_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"] stability_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"]
outcome_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"] outcome_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"]
@ -162,7 +171,8 @@ function(input, output, session) {
### NGLViewer #### ### NGLViewer ####
# Structure Viewer WebGL/NGLViewR window # Structure Viewer WebGL/NGLViewR window
output$structure <- renderNGLVieweR({ output$structure <- renderNGLVieweR({
ngl_gene=isolate(input$switch_target) #ngl_gene=isolate(input$switch_target)
ngl_gene=input$switch_target
ngl_drug=target_map[[ngl_gene]] ngl_drug=target_map[[ngl_gene]]
ngl_pdb_file=paste0(load_dir, "Data/", ngl_drug, '/output/depth/', ngl_gene, '_complex.pdb') ngl_pdb_file=paste0(load_dir, "Data/", ngl_drug, '/output/depth/', ngl_gene, '_complex.pdb')
print(ngl_pdb_file) print(ngl_pdb_file)
@ -262,6 +272,8 @@ function(input, output, session) {
geom_ls = 4 geom_ls = 4
) )
) )
# if ("interface_dist" %in% colnames(input$switch_target)) {
output$site_snp_count_interface = renderPlot( output$site_snp_count_interface = renderPlot(
site_snp_count_bp( site_snp_count_bp(
snp_interface_dist_df3, snp_interface_dist_df3,
@ -272,7 +284,14 @@ function(input, output, session) {
geom_ls = 4 geom_ls = 4
) )
) )
output$site_snp_count_nca = renderPlot( # } #else {
# output$site_snp_count_interface = renderPlot(
# ggplot() + annotate(x=1,y=1,"text", label="No interface data for this target")+theme_void()
# )
# }
output$site_snp_count_nca = renderPlot( #{
#if ("nca_distance" %in% colnames(input$switch_target)) {
site_snp_count_bp( site_snp_count_bp(
snp_nca_dist_df3, snp_nca_dist_df3,
title_colour = 'black', title_colour = 'black',
@ -281,8 +300,14 @@ function(input, output, session) {
axis_label_size = 12, axis_label_size = 12,
geom_ls = 4 geom_ls = 4
) )
# } else {
# ggplot() + annotate(x=1,y=1,"text", label="No RNA data for this target")+theme_void()
# }
# }
) )
#### DM OM Plots #### #### DM OM Plots ####
#dm_om_param #dm_om_param
# order needs to be: # order needs to be:

2
drug-target/ui.R
View file

@ -292,7 +292,7 @@ dashboardPage(skin="purple",
column(conditionalPanel( column(conditionalPanel(
condition="input.sidebar == 'Site SNP count'", condition="input.sidebar == 'Site SNP count'",
box( box(
title="NCA Distance" title="RNA Distance"
, status = "info" , status = "info"
, width=NULL , width=NULL
, plotOutput("site_snp_count_nca") %>% withSpinner(color="#0dc5c1") , plotOutput("site_snp_count_nca") %>% withSpinner(color="#0dc5c1")