tanu/Dashboards
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

msa

Browse source
This commit is contained in:
Tanushree Tunstall 2022-09-05 16:57:00 +01:00
parent e69c2a60aa
commit 594c1c24d6
1 changed files with 173 additions and 169 deletions
Download patch file Download diff file Expand all files Collapse all files

316
msa/global.R
View file

@ -31,7 +31,11 @@ library(hash)
# than previous approaches # than previous approaches
# system.time({ # system.time({
source("~/git/LSHTM_analysis/scripts/Header_TT.R") if(interactive()){
source("~/git/LSHTM_analysis/scripts/Header_TT.R")
} else {
source("/srv/shiny-server/git/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))
@ -248,182 +252,182 @@ lapply(c(
#### Shiny UI ##### #### Shiny UI #####
if(interactive()){ if(interactive()){
ui <- dashboardPage( ui <- dashboardPage(
#dashboardHeader(title = paste0(gene, "/", drug)), #dashboardHeader(title = paste0(gene, "/", drug)),
dashboardHeader(title = "Sequence Alignment"), dashboardHeader(title = "Sequence Alignment"),
dashboardSidebar( dashboardSidebar(
sidebarMenu( id = "sidebar", sidebarMenu( id = "sidebar",
selectInput( selectInput(
"switch_target", "switch_target",
label="Target", label="Target",
choices = c( choices = c(
"alr", "alr",
"embb", "embb",
"gid", "gid",
"katg", "katg",
"pnca", "pnca",
"rpob" "rpob"
),
selected="embb"),
menuItem("LogoP ED", tabName="LogoP ED"),
sliderInput(
"display_position_full_range"
, "Display Positions"
, min=1, max=150, value=c(1,150)
), ),
selected="embb"),
menuItem("LogoP ED", tabName="LogoP ED"),
sliderInput( conditionalPanel(
"display_position_full_range" condition="
, "Display Positions"
, min=1, max=150, value=c(1,150)
),
conditionalPanel(
condition="
input.sidebar == 'LogoP SNP' || input.sidebar == 'LogoP SNP' ||
input.sidebar == 'LogoP OR' || input.sidebar == 'LogoP OR' ||
input.sidebar == 'LogoP ED'", input.sidebar == 'LogoP ED'",
selectInput( selectInput(
"logoplot_colour_scheme", "logoplot_colour_scheme",
label="Logo Plot Colour Scheme", label="Logo Plot Colour Scheme",
choices = logoPlotSchemes, choices = logoPlotSchemes,
selected="chemistry" selected="chemistry"
)
) )
)
)
),
body <- dashboardBody(
tabItems(
tabItem(tabName = "dashboard",
h2("Dashboard tab content")
),
tabItem(tabName = "widgets",
h2("Widgets tab content")
) )
), ),
# creates a 'Conditional Panel' containing a plot object from each of our body <- dashboardBody(
# ggplot plot functions (and its associated data frame)
fluidRow( tabItems(
column( tabItem(tabName = "dashboard",
width=12, h2("Dashboard tab content")
plotOutput("LogoPlotMSA", ),
click = "plot_click") %>% withSpinner(color="#0dc5c1")
tabItem(tabName = "widgets",
h2("Widgets tab content")
)
),
# creates a 'Conditional Panel' containing a plot object from each of our
# ggplot plot functions (and its associated data frame)
fluidRow(
column(
width=12,
plotOutput("LogoPlotMSA",
click = "plot_click") %>% withSpinner(color="#0dc5c1")
)
) )
) )
) )
) #### Shiny Backend Server #####
#### Shiny Backend Server ##### server <- function(input, output, session) {
server <- function(input, output, session) { observeEvent(
observeEvent( {
{ input$display_position_full_range #special-purpose for MSA
input$display_position_full_range #special-purpose for MSA input$logoplot_colour_scheme
input$logoplot_colour_scheme input$switch_target
input$switch_target },
}, {
{ # 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]] 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']])
position_min=min(merged_df3[['position']]) position_min=min(merged_df3[['position']])
min_ligand_distance=min(merged_df3$ligand_distance) min_ligand_distance=min(merged_df3$ligand_distance)
max_ligand_distance=max(merged_df3$ligand_distance) max_ligand_distance=max(merged_df3$ligand_distance)
# FIXME: these are IMPORTANT # FIXME: these are IMPORTANT
# # add "pos_count" position count column # # add "pos_count" position count column
# merged_df3=merged_df3 %>% dplyr::add_count(position) # merged_df3=merged_df3 %>% dplyr::add_count(position)
# merged_df3$pos_count=merged_df3$n # merged_df3$pos_count=merged_df3$n
# merged_df3$n=NULL # merged_df3$n=NULL
# #
mutable_df3 = cbind(merged_df3) mutable_df3 = cbind(merged_df3)
unified_msa = get(paste0(input$switch_target, '_unified_msa')) unified_msa = get(paste0(input$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("~/git/Data/", drug, '/output/')
indir = paste0("~/git/Data/", drug , "/input/") indir = paste0("~/git/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...
# source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") # source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#### nasty special-purpose merged_df3 variants #### #### nasty special-purpose merged_df3 variants ####
# FIXME: SLOW # FIXME: SLOW
# corr_plotdf = corr_data_extract( # corr_plotdf = corr_data_extract(
# merged_df3 # merged_df3
# , gene = gene # , gene = gene
# , drug = drug # , drug = drug
# , extract_scaled_cols = F # , extract_scaled_cols = F
# ) # )
#input$stability_snp_param #input$stability_snp_param
updateSliderInput( updateSliderInput(
session, session,
"display_position_range", "display_position_range",
min = position_min, min = position_min,
max = position_max max = position_max
#, value = c(position_min, position_min+150) #, value = c(position_min, position_min+150)
)
updateSliderInput(
session,
"display_position_full_range",
min = 1,
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,
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
) )
) updateSliderInput(
} session,
) "display_position_full_range",
min = 1,
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)
#### EOF Shiny Server #### 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 ####
################ Running Server ############## output$LogoPlotMSA = renderPlot(
app <- shinyApp(ui, server) LogoPlotMSA(target=input$switch_target,
plot_positions=full_range_min:full_range_max,
my_logo_col = logoplot_colour_scheme,
runApp(app) 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
)
)
}
)
#### EOF Shiny Server ####
}
################ Running Server ##############
app <- shinyApp(ui, server)
runApp(app)
} }