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wholesale change for Header_TT.R location

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Tanushree Tunstall 2022-01-26 11:39:03 +00:00
parent b133b8be24
commit 586927ca56
46 changed files with 46 additions and 46 deletions
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2
scripts/af_or_calcs.R
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@ -8,7 +8,7 @@ setwd("~/git/LSHTM_analysis/scripts")
getwd() getwd()
# load libraries # load libraries
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
require("getopt", quietly = TRUE) # cmd parse arguments require("getopt", quietly = TRUE) # cmd parse arguments
# load functions # load functions

2
scripts/functions/combining_dfs_plotting.R
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@ -6,7 +6,7 @@
########################################################### ###########################################################
# load libraries and functions # load libraries and functions
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
#========================================================== #==========================================================
# combining_dfs_plotting(): # combining_dfs_plotting():

2
scripts/functions/tests/test_af_or_calcs.R
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@ -4,7 +4,7 @@
# Odds Ratio from master data # Odds Ratio from master data
######################################################### #########################################################
# load libraries # load libraries
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
require("getopt", quietly = TRUE) # cmd parse arguments require("getopt", quietly = TRUE) # cmd parse arguments
# working dir and loading libraries # working dir and loading libraries

2
scripts/functions/tests/test_lf_bp.R
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@ -1,5 +1,5 @@
setwd("~/git/LSHTM_analysis/scripts/plotting/") setwd("~/git/LSHTM_analysis/scripts/plotting/")
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
source("../functions/lf_bp.R") source("../functions/lf_bp.R")
# ================================================ # ================================================
# Data: run get_plotting_data.R # Data: run get_plotting_data.R

2
scripts/functions/tests/test_lineage_dist.R
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@ -7,7 +7,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/") setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
source("get_plotting_dfs.R") source("get_plotting_dfs.R")

2
scripts/plotting/TESTING_PLOTS.R
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@ -2,7 +2,7 @@
getwd() getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
drug = 'streptomycin' drug = 'streptomycin'
gene = 'gid' gene = 'gid'

2
scripts/plotting/barplots_subcolours.R
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@ -2,7 +2,7 @@
getwd() getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
drug = 'streptomycin' drug = 'streptomycin'
gene = 'gid' gene = 'gid'

2
scripts/plotting/barplots_subcolours_aa_LIG.R
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@ -15,7 +15,7 @@ getwd()
# 1: Installing and loading required packages and functions # 1: Installing and loading required packages and functions
############################################################ ############################################################
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
source("../functions/bp_subcolours.R") source("../functions/bp_subcolours.R")

2
scripts/plotting/barplots_subcolours_aa_PS.R
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@ -14,7 +14,7 @@ getwd()
# 1: Installing and loading required packages and functions # 1: Installing and loading required packages and functions
############################################################ ############################################################
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
source("../functions/bp_subcolours.R") source("../functions/bp_subcolours.R")

2
scripts/plotting/basic_barplots.R
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@ -9,7 +9,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
# load libraries # load libraries
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
library(dplyr) library(dplyr)

2
scripts/plotting/corr_adjusted_PS_LIG.R
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@ -11,7 +11,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
require(cowplot) require(cowplot)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
source("my_pairs_panel.R") source("my_pairs_panel.R")

2
scripts/plotting/corr_plots.R
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@ -2,7 +2,7 @@
getwd() getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
spec = matrix(c( spec = matrix(c(
"drug" , "d", 1, "character", "drug" , "d", 1, "character",

2
scripts/plotting/dist_plots_check.R
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@ -9,7 +9,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(tidyverse) library(tidyverse)
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)

2
scripts/plotting/extreme_muts.R
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@ -10,7 +10,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(tidyverse) library(tidyverse)
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)

2
scripts/plotting/get_plotting_dfs_with_lig.R
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@ -7,7 +7,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
source("../functions/my_pairs_panel.R") # with lower panel turned off source("../functions/my_pairs_panel.R") # with lower panel turned off
source("../functions/plotting_globals.R") source("../functions/plotting_globals.R")
source("../functions/plotting_data.R") source("../functions/plotting_data.R")

2
scripts/plotting/ggcorr_all_PS_LIG.R
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@ -10,7 +10,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/") setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
require(cowplot) require(cowplot)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
#source("my_pairs_panel.R") #source("my_pairs_panel.R")

2
scripts/plotting/hist_af_or_base.R
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@ -16,7 +16,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
library(dplyr) library(dplyr)

2
scripts/plotting/hist_af_or_combined.R
View file

@ -16,7 +16,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
library(dplyr) library(dplyr)

2
scripts/plotting/lineage_basic_barplot.R
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@ -10,7 +10,7 @@ getwd()
########################################################## ##########################################################
# Installing and loading required packages # Installing and loading required packages
########################################################## ##########################################################
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
require(data.table) require(data.table)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
# should return the following dfs, directories and variables # should return the following dfs, directories and variables

2
scripts/plotting/lineage_basic_barplots_combined.R
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@ -11,7 +11,7 @@ getwd()
########################################################## ##########################################################
# Installing and loading required packages # Installing and loading required packages
########################################################## ##########################################################
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
#=========== #===========
# input # input

2
scripts/plotting/lineage_dist_combined_PS.R
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@ -14,7 +14,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/") setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggridges) library(ggridges)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
# PS combined: # PS combined:

2
scripts/plotting/lineage_dist_dm_om_combined_PS.R
View file

@ -14,7 +14,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/") setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggridges) library(ggridges)
library(plyr) library(plyr)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")

2
scripts/plotting/lineage_dist_plots.R
View file

@ -11,7 +11,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/") setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") # also loads all my functions source("~/git/LSHTM_analysis/scripts/Header_TT.R") # also loads all my functions
#=========== #===========
# input # input

2
scripts/plotting/logo_plots.R
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@ -15,7 +15,7 @@
getwd() getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
spec = matrix(c( spec = matrix(c(
"drug" , "d", 1, "character", "drug" , "d", 1, "character",

2
scripts/plotting/mcsm_mean_stability.R
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@ -6,7 +6,7 @@ getwd()
# TASK: # TASK:
######################################################### #########################################################
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
#require(data.table) #require(data.table)
#require(dplyr) #require(dplyr)

2
scripts/plotting/myshiny/subcols_bp.R
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@ -6,7 +6,7 @@ library(shinyBS)
getwd() getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
drug = 'streptomycin' drug = 'streptomycin'
gene = 'gid' gene = 'gid'

2
scripts/plotting/or_plots_combined.R
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@ -11,7 +11,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
require(cowplot) require(cowplot)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
# should return the following dfs, directories and variables # should return the following dfs, directories and variables

2
scripts/plotting/other_plots_combined.R
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@ -9,7 +9,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
#library(ggplot2) #library(ggplot2)
#library(data.table) #library(data.table)
#library(dplyr) #library(dplyr)

2
scripts/plotting/other_plots_data.R
View file

@ -9,7 +9,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
library(dplyr) library(dplyr)

2
scripts/plotting/output_tables.R
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@ -9,7 +9,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
library(dplyr) library(dplyr)

2
scripts/plotting/ps_plots_combined.R
View file

@ -10,7 +10,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
#source("combining_dfs_plotting.R") #source("combining_dfs_plotting.R")

2
scripts/plotting/redundant/barplots_subcolours_PS.R
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@ -12,7 +12,7 @@ getwd()
# 1: Installing and loading required packages and functions # 1: Installing and loading required packages and functions
############################################################# #############################################################
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
source("barplot_colour_function.R") source("barplot_colour_function.R")

2
scripts/plotting/redundant/basic_barplots_LIG.R
View file

@ -14,7 +14,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
# load libraries # load libraries
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
library(dplyr) library(dplyr)

2
scripts/plotting/redundant/basic_barplots_PS.R
View file

@ -14,7 +14,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
# load libraries # load libraries
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
library(dplyr) library(dplyr)

2
scripts/plotting/redundant/combining_dfs_plotting.R
View file

@ -27,7 +27,7 @@ getwd()
require("getopt", quietly = TRUE) # cmd parse arguments require("getopt", quietly = TRUE) # cmd parse arguments
# load functions # load functions
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
source("../functions/plotting_globals.R") source("../functions/plotting_globals.R")
source("../functions/plotting_data.R") source("../functions/plotting_data.R")

2
scripts/plotting/redundant/combining_two_df_FIXME.R
View file

@ -24,7 +24,7 @@ getwd()
########################################################## ##########################################################
# Installing and loading required packages # Installing and loading required packages
########################################################## ##########################################################
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
#require(data.table) #require(data.table)
#require(arsenal) #require(arsenal)
#require(compare) #require(compare)

2
scripts/plotting/redundant/corr_PS_LIG.R
View file

@ -11,7 +11,7 @@ setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
require(cowplot) require(cowplot)
source("../functions/combining_dfs_plotting.R") source("../functions/combining_dfs_plotting.R")

2
scripts/plotting/redundant/corr_data.R
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@ -8,7 +8,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
source("../functions/my_pairs_panel.R") # with lower panel turned off source("../functions/my_pairs_panel.R") # with lower panel turned off
source("../functions/plotting_globals.R") source("../functions/plotting_globals.R")
source("../functions/plotting_data.R") source("../functions/plotting_data.R")

2
scripts/plotting/redundant/lineage_basic_barplot.R
View file

@ -10,7 +10,7 @@ getwd()
########################################################## ##########################################################
# Installing and loading required packages # Installing and loading required packages
########################################################## ##########################################################
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
require(data.table) require(data.table)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
# should return the following dfs, directories and variables # should return the following dfs, directories and variables

2
scripts/plotting/redundant/lineage_dist_combined_PS.R
View file

@ -14,7 +14,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/") setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggridges) library(ggridges)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
# PS combined: # PS combined:

2
scripts/plotting/redundant/lineage_dist_dm_om_combined_PS.R
View file

@ -14,7 +14,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/") setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
source("get_plotting_dfs.R") source("get_plotting_dfs.R")

2
scripts/plotting/redundant/logo_multiple_muts.R
View file

@ -2,7 +2,7 @@
getwd() getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
spec = matrix(c( spec = matrix(c(
"drug" , "d", 1, "character", "drug" , "d", 1, "character",

2
scripts/plotting/redundant/logo_plot.R
View file

@ -2,7 +2,7 @@
getwd() getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
spec = matrix(c( spec = matrix(c(
"drug" , "d", 1, "character", "drug" , "d", 1, "character",

2
scripts/plotting/redundant/other_plots_data_SAFEGUARD.R
View file

@ -9,7 +9,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd() getwd()
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggplot2) library(ggplot2)
library(data.table) library(data.table)
library(dplyr) library(dplyr)

2
scripts/plotting/replaceBfactor_pdb.R
View file

@ -21,7 +21,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting") setwd("~/git/LSHTM_analysis/scripts/plotting")
cat(c(getwd(),"\n")) cat(c(getwd(),"\n"))
#source("Header_TT.R") #source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(bio3d) library(bio3d)
require("getopt", quietly = TRUE) # cmd parse arguments require("getopt", quietly = TRUE) # cmd parse arguments
#======================================================== #========================================================

2
scripts/plotting/scratch_plots/lineage_dist_dm_om_PS.R
View file

@ -14,7 +14,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/") setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd() getwd()
source("Header_TT.R") source("~/git/LSHTM_analysis/scripts/Header_TT.R")
library(ggridges) library(ggridges)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
# PS combined: # PS combined: