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Tanushree Tunstall 2022-10-10 15:57:54 +01:00
parent c4432dd490
commit 70f8a917e5
1 changed files with 104 additions and 79 deletions
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183
drug-target/server.R
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@ -44,7 +44,110 @@ function(input, output, session) {
, color = "green")
)
})
observeEvent(
{
input$switch_target
input$snp_ligand_dist
input$snp_nca_dist
input$snp_interface_dist
},{
target_gene = input$switch_target
merged_df3 = cbind(get(paste0(input$switch_target, '_merged_df3')))
position_max=max(merged_df3[['position']])
position_min=min(merged_df3[['position']])
min_ligand_distance=min(merged_df3$ligand_distance)
max_ligand_distance=max(merged_df3$ligand_distance)
# FIXME: these are IMPORTANT
# # add "pos_count" position count column
# merged_df3=merged_df3 %>% dplyr::add_count(position)
# merged_df3$pos_count=merged_df3$n
# merged_df3$n=NULL
#
mutable_df3 = cbind(merged_df3)
#### site_snp_count_bp ####
#mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
# ligand_distance
# interface_dist
# nca_distance
# change to: multiple plots, all use site_snp_count_bp
# 4 x plots side by side, one normal (no dist. filter), 2/3 filtered by distance columns above
# use "subtitle text" from pos_count_bp_i.R
# different data ranges required for SNP distances
snp_ligand_dist_df3 = merged_df3[merged_df3[['ligand_distance']]<input$snp_ligand_dist,]
if ("interface_dist" %in% colnames(merged_df3)){
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
}
output$site_snp_count_bp = renderPlot(
site_snp_count_bp(
mutable_df3,
title_colour = 'black',
subtitle_colour = "black",
leg_text_size = 12,
axis_label_size = 12,
geom_ls = 4
)
)
output$site_snp_count_bp_ligand = renderPlot(
site_snp_count_bp(
snp_ligand_dist_df3,
title_colour = 'black',
subtitle_colour = "black",
leg_text_size = 12,
axis_label_size = 12,
geom_ls = 4
)
)
# if ("interface_dist" %in% colnames(input$switch_target)) {
output$site_snp_count_interface = renderPlot(
site_snp_count_bp(
snp_interface_dist_df3,
title_colour = 'black',
subtitle_colour = "black",
leg_text_size = 12,
axis_label_size = 12,
geom_ls = 4
)
)
# } #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$switch_target)) {
site_snp_count_bp(
snp_nca_dist_df3,
title_colour = 'black',
subtitle_colour = "black",
leg_text_size = 12,
axis_label_size = 12,
geom_ls = 4
)
# } else {
# ggplot() + annotate(x=1,y=1,"text", label="No RNA data for this target")+theme_void()
# }
# }
)
}
)
observeEvent(
{
input$display_position_range
@ -52,9 +155,6 @@ function(input, output, session) {
input$logoplot_colour_scheme
input$omit_snp_count
input$switch_target
input$snp_ligand_dist
input$snp_nca_dist
input$snp_interface_dist
input$force
},
{
@ -122,19 +222,6 @@ function(input, output, session) {
updateNumericInput(session, "snp_nca_dist", min = min(merged_df3$nca_distance), max = max(merged_df3$nca_distance))
# different data ranges required for SNP distances
snp_ligand_dist_df3 = merged_df3[merged_df3[['ligand_distance']]<input$snp_ligand_dist,]
if ("interface_dist" %in% colnames(merged_df3)){
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"]
outcome_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"]
@ -242,68 +329,6 @@ function(input, output, session) {
)
)
#### site_snp_count_bp ####
#mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
# ligand_distance
# interface_dist
# nca_distance
# change to: multiple plots, all use site_snp_count_bp
# 4 x plots side by side, one normal (no dist. filter), 2/3 filtered by distance columns above
# use "subtitle text" from pos_count_bp_i.R
output$site_snp_count_bp = renderPlot(
site_snp_count_bp(
mutable_df3,
title_colour = 'black',
subtitle_colour = "black",
leg_text_size = 12,
axis_label_size = 12,
geom_ls = 4
)
)
output$site_snp_count_bp_ligand = renderPlot(
site_snp_count_bp(
snp_ligand_dist_df3,
title_colour = 'black',
subtitle_colour = "black",
leg_text_size = 12,
axis_label_size = 12,
geom_ls = 4
)
)
# if ("interface_dist" %in% colnames(input$switch_target)) {
output$site_snp_count_interface = renderPlot(
site_snp_count_bp(
snp_interface_dist_df3,
title_colour = 'black',
subtitle_colour = "black",
leg_text_size = 12,
axis_label_size = 12,
geom_ls = 4
)
)
# } #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(
snp_nca_dist_df3,
title_colour = 'black',
subtitle_colour = "black",
leg_text_size = 12,
axis_label_size = 12,
geom_ls = 4
)
# } else {
# ggplot() + annotate(x=1,y=1,"text", label="No RNA data for this target")+theme_void()
# }
# }
)