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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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51
msa/server.R
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@ -9,6 +9,7 @@ function(input, output, session) {
# C O M P A T I B I L I T Y
#gene=input$switch_target
#drug=target_map[[gene]]
target = input$switch_target
merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3')))
position_max=max(merged_df3[['position']])
@ -22,15 +23,14 @@ function(input, output, session) {
# merged_df3$n=NULL
#
mutable_df3 = cbind(merged_df3)
unified_msa = get(paste0(input$switch_target, '_unified_msa'))
#
# # re-sort the dataframe according to position count
sorted_df = cbind(merged_df3)
sorted_df = sorted_df %>% arrange(pos_count)
#
outdir = paste0("~/git/Data/", drug, '/output/')
indir = paste0("~/git/Data/", drug , "/input/")
outdir = paste0(load_dir, "Data/", drug, '/output/')
indir = paste0(load_dir, "Data/", drug , "/input/")
#
# source("~/git/LSHTM_analysis/scripts/plotting/logo_data_msa.R") # probably unnecessary...
@ -47,13 +47,7 @@ function(input, output, session) {
#input$stability_snp_param
updateSliderInput(
session,
"display_position_range",
min = position_min,
max = position_max
#, value = c(position_min, position_min+150)
)
updateSliderInput(
session,
"display_position_full_range",
@ -61,45 +55,30 @@ function(input, output, session) {
max = position_max #,
# 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
full_range_min=display_position_full_range[1]
full_range_max=display_position_full_range[2]
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 ####
output$LogoPlotMSA = renderPlot(
LogoPlotMSA(target=input$switch_target,
LogoPlotMSA(target=target,
plot_positions=full_range_min:full_range_max,
my_logo_col = logoplot_colour_scheme,
aa_pos_drug = aa_pos_drug,
active_aa_pos = active_aa_pos,
aa_pos_lig1 = aa_pos_lig1,
aa_pos_lig2 = aa_pos_lig2,
aa_pos_lig3 = aa_pos_lig3
aa_pos_drug = paste0(target,"_aa_pos_drug"),
active_aa_pos = paste0(target,"_active_aa_pos"),
aa_pos_lig1 = paste0(target,"_aa_pos_lig1"),
aa_pos_lig2 = paste0(target,"_aa_pos_lig2"),
aa_pos_lig3 = paste0(target,"_aa_pos_lig3")
)
)
}
)
#### EOF Shiny Server ####
}