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msa dash

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Tanushree Tunstall 2022-09-05 18:49:20 +01:00
parent 75ec1419d7
commit 904798bb60
2 changed files with 38 additions and 90 deletions
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77
msa/global.R
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@ -42,8 +42,13 @@ source(paste0(load_dir,"LSHTM_analysis/scripts/Header_TT.R"))
load_target_globals=function(target){ load_target_globals=function(target){
cat(paste0("Reloading Target: ", target)) cat(paste0("Reloading Target: ", target))
source(paste0(load_dir, "LSHTM_analysis/config/", target, ".R")) # load per-target config file source(paste0(load_dir, "LSHTM_analysis/config/", target, ".R")) # load per-target config file
invisible(assign(paste0(target, "_aa_pos_drug"), aa_pos_drug, envir = .GlobalEnv))
invisible(assign(paste0(target, "_active_aa_pos"), active_aa_pos, envir = .GlobalEnv))
invisible(assign(paste0(target, "_aa_pos_lig1"), aa_pos_lig1, envir = .GlobalEnv))
invisible(assign(paste0(target, "_aa_pos_lig2"), aa_pos_lig2, envir = .GlobalEnv))
invisible(assign(paste0(target, "_aa_pos_lig3"), aa_pos_lig3, envir = .GlobalEnv))
invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv)) invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv)) invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_corr_df_m3_f"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.csv")), envir = .GlobalEnv)) invisible(assign(paste0(target, "_corr_df_m3_f"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.csv")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_lin_lf"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-lin_lf.csv")), envir = .GlobalEnv)) invisible(assign(paste0(target, "_lin_lf"), read.csv(paste0(load_dir, "Misc/shiny_dashboard/data/",target,"-lin_lf.csv")), envir = .GlobalEnv))
@ -96,24 +101,7 @@ load_msa_global=function(gene){
#### Local Functions #### #### Local Functions ####
# FIXME: passing in the per-plot params is broken
lin_sc=function(x, all_lineages = F, ...){
lf_var = get(paste0(x,"_lin_lf"))
wf_var = get(paste0(x,"_lin_wf"))
cowplot::plot_grid(lin_count_bp_diversity(wf_var, all_lineages, ...), lin_count_bp(lf_var, all_lineages, ...))
}
options(shiny.port = 8000)
options(shiny.host = '0.0.0.0') # This means "listen to all addresses on all interfaces"
options(shiny.launch.browser = FALSE)
options(width=120)
options(DT.options = list(scrollX = TRUE))
################ STATIC GLOBALS ONLY ############## ################ STATIC GLOBALS ONLY ##############
# never quite sure where "outdir" gets set :-|
# using dataframes instead of lists lets us avoid use of map() # using dataframes instead of lists lets us avoid use of map()
plot_functions_df=data.frame( plot_functions_df=data.frame(
@ -254,6 +242,13 @@ lapply(c(
#### Shiny UI ##### #### Shiny UI #####
if(interactive()){ if(interactive()){
options(shiny.port = 8000)
options(shiny.host = '0.0.0.0') # This means "listen to all addresses on all interfaces"
options(shiny.launch.browser = FALSE)
options(width=120)
options(DT.options = list(scrollX = TRUE))
ui <- dashboardPage( ui <- dashboardPage(
#dashboardHeader(title = paste0(gene, "/", drug)), #dashboardHeader(title = paste0(gene, "/", drug)),
dashboardHeader(title = "Sequence Alignment"), dashboardHeader(title = "Sequence Alignment"),
@ -328,6 +323,7 @@ if(interactive()){
# C O M P A T I B I L I T Y # C O M P A T I B I L I T Y
#gene=input$switch_target #gene=input$switch_target
#drug=target_map[[gene]] #drug=target_map[[gene]]
target = input$switch_target
merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3'))) merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3')))
position_max=max(merged_df3[['position']]) position_max=max(merged_df3[['position']])
@ -341,7 +337,6 @@ if(interactive()){
# merged_df3$n=NULL # merged_df3$n=NULL
# #
mutable_df3 = cbind(merged_df3) mutable_df3 = cbind(merged_df3)
unified_msa = get(paste0(input$switch_target, '_unified_msa'))
# #
# # re-sort the dataframe according to position count # # re-sort the dataframe according to position count
sorted_df = cbind(merged_df3) sorted_df = cbind(merged_df3)
@ -366,13 +361,7 @@ if(interactive()){
#input$stability_snp_param #input$stability_snp_param
updateSliderInput(
session,
"display_position_range",
min = position_min,
max = position_max
#, value = c(position_min, position_min+150)
)
updateSliderInput( updateSliderInput(
session, session,
"display_position_full_range", "display_position_full_range",
@ -380,43 +369,23 @@ if(interactive()){
max = position_max #, max = position_max #,
# value = c(position_min, position_min+150) # value = c(position_min, position_min+150)
) )
updateNumericInput(session, "selected_logop_snp_position", min = position_min, max = position_max, value = position_min)
updateNumericInput(session, "selected_logop_ed_position", min = position_min, max = position_max, value = position_min)
updateNumericInput(session, "corr_lig_dist", min = min_ligand_distance, max = max_ligand_distance, value = min_ligand_distance)
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"]
display_position_range = input$display_position_range
plot_min=display_position_range[1]
plot_max=display_position_range[2]
display_position_full_range = input$display_position_full_range display_position_full_range = input$display_position_full_range
full_range_min=display_position_full_range[1] full_range_min=display_position_full_range[1]
full_range_max=display_position_full_range[2] full_range_max=display_position_full_range[2]
logoplot_colour_scheme = input$logoplot_colour_scheme logoplot_colour_scheme = input$logoplot_colour_scheme
omit_snp_count = input$omit_snp_count
print(paste0('Plotting positions between: ', plot_min, ' and ', plot_max))
subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
subset_sorted_df=sorted_df[(sorted_df$position>=plot_min & sorted_df$position <=plot_max),]
#### LogoPlotMSA/Logo Plot ED #### #### LogoPlotMSA/Logo Plot ED ####
output$LogoPlotMSA = renderPlot( output$LogoPlotMSA = renderPlot(
LogoPlotMSA(target=input$switch_target, LogoPlotMSA(target=target,
plot_positions=full_range_min:full_range_max, plot_positions=full_range_min:full_range_max,
my_logo_col = logoplot_colour_scheme, my_logo_col = logoplot_colour_scheme,
aa_pos_drug = aa_pos_drug, aa_pos_drug = paste0(target,"_aa_pos_drug"),
active_aa_pos = active_aa_pos, active_aa_pos = paste0(target,"_active_aa_pos"),
aa_pos_lig1 = aa_pos_lig1, aa_pos_lig1 = paste0(target,"_aa_pos_lig1"),
aa_pos_lig2 = aa_pos_lig2, aa_pos_lig2 = paste0(target,"_aa_pos_lig2"),
aa_pos_lig3 = aa_pos_lig3 aa_pos_lig3 = paste0(target,"_aa_pos_lig3")
) )
) )
} }

51
msa/server.R
View file

@ -9,6 +9,7 @@ function(input, output, session) {
# C O M P A T I B I L I T Y # C O M P A T I B I L I T Y
#gene=input$switch_target #gene=input$switch_target
#drug=target_map[[gene]] #drug=target_map[[gene]]
target = input$switch_target
merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3'))) merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3')))
position_max=max(merged_df3[['position']]) position_max=max(merged_df3[['position']])
@ -22,15 +23,14 @@ function(input, output, session) {
# merged_df3$n=NULL # merged_df3$n=NULL
# #
mutable_df3 = cbind(merged_df3) mutable_df3 = cbind(merged_df3)
unified_msa = get(paste0(input$switch_target, '_unified_msa'))
# #
# # re-sort the dataframe according to position count # # re-sort the dataframe according to position count
sorted_df = cbind(merged_df3) sorted_df = cbind(merged_df3)
sorted_df = sorted_df %>% arrange(pos_count) sorted_df = sorted_df %>% arrange(pos_count)
# #
outdir = paste0("~/git/Data/", drug, '/output/') outdir = paste0(load_dir, "Data/", drug, '/output/')
indir = paste0("~/git/Data/", drug , "/input/") indir = paste0(load_dir, "Data/", drug , "/input/")
# #
# source("~/git/LSHTM_analysis/scripts/plotting/logo_data_msa.R") # probably unnecessary... # source("~/git/LSHTM_analysis/scripts/plotting/logo_data_msa.R") # probably unnecessary...
@ -47,13 +47,7 @@ function(input, output, session) {
#input$stability_snp_param #input$stability_snp_param
updateSliderInput(
session,
"display_position_range",
min = position_min,
max = position_max
#, value = c(position_min, position_min+150)
)
updateSliderInput( updateSliderInput(
session, session,
"display_position_full_range", "display_position_full_range",
@ -61,45 +55,30 @@ function(input, output, session) {
max = position_max #, max = position_max #,
# value = c(position_min, position_min+150) # value = c(position_min, position_min+150)
) )
updateNumericInput(session, "selected_logop_snp_position", min = position_min, max = position_max, value = position_min)
updateNumericInput(session, "selected_logop_ed_position", min = position_min, max = position_max, value = position_min)
updateNumericInput(session, "corr_lig_dist", min = min_ligand_distance, max = max_ligand_distance, value = min_ligand_distance)
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"]
display_position_range = input$display_position_range
plot_min=display_position_range[1]
plot_max=display_position_range[2]
display_position_full_range = input$display_position_full_range display_position_full_range = input$display_position_full_range
full_range_min=display_position_full_range[1] full_range_min=display_position_full_range[1]
full_range_max=display_position_full_range[2] full_range_max=display_position_full_range[2]
logoplot_colour_scheme = input$logoplot_colour_scheme logoplot_colour_scheme = input$logoplot_colour_scheme
omit_snp_count = input$omit_snp_count
print(paste0('Plotting positions between: ', plot_min, ' and ', plot_max))
subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
subset_sorted_df=sorted_df[(sorted_df$position>=plot_min & sorted_df$position <=plot_max),]
#### LogoPlotMSA/Logo Plot ED #### #### LogoPlotMSA/Logo Plot ED ####
output$LogoPlotMSA = renderPlot( output$LogoPlotMSA = renderPlot(
LogoPlotMSA(target=input$switch_target, LogoPlotMSA(target=target,
plot_positions=full_range_min:full_range_max, plot_positions=full_range_min:full_range_max,
my_logo_col = logoplot_colour_scheme, my_logo_col = logoplot_colour_scheme,
aa_pos_drug = aa_pos_drug, aa_pos_drug = paste0(target,"_aa_pos_drug"),
active_aa_pos = active_aa_pos, active_aa_pos = paste0(target,"_active_aa_pos"),
aa_pos_lig1 = aa_pos_lig1, aa_pos_lig1 = paste0(target,"_aa_pos_lig1"),
aa_pos_lig2 = aa_pos_lig2, aa_pos_lig2 = paste0(target,"_aa_pos_lig2"),
aa_pos_lig3 = aa_pos_lig3 aa_pos_lig3 = paste0(target,"_aa_pos_lig3")
) )
) )
} }
) )
#### EOF Shiny Server ####
} }