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pwd()
getwd()
R.version
citation()
source("~/Documents/smith/labbook/roessler_netzl_et_al2023/code/ablandscape_fit_multi.R")
source("~/Documents/smith/labbook/roessler_netzl_et_al2023/code/ablandscape_fit_idvl.R")
source("~/Documents/smith/labbook/roessler_netzl_et_al2023/code/ablandscape_fit_multi.R")
titertables_groups$sr_group
lndscp_list <- list()
data3js <- base_plot_data3js(map, lndscp_fits, agNames(map), lims, agNames(map))
# do plot with D614G conv., BNT/BNT and BNT/BNT/BNT
lndscp_3js <- plot_landscapes_from_list(data3js, titertables_groups[c(1:3),], lndscp_fits[c(1:3)], map, gmt_data, agNames(map), agNames(map), lndscp_colors = sr_colors)
lndscp <-r3js(
lndscp_3js,
rotation = angle$rotation,
zoom = angle$zoom
)
lndscp_list[["Vacc_Anc."]] <- lndscp
ldnscp
lndscp
save_name <- file.path(figure_dir, paste0(fit_ags, "vacc_anc_gmt"))
plot_single_landscape_panel(lndscp, label = "", save_name = save_name, delete_html = FALSE)
lndscp
lndscp <-r3js(
lndscp_3js,
rotation = c(-1.5836, 0.0100, -0.0131),
zoom = angle$zoom
)
lndscp_list[["Vacc_Anc."]] <- lndscp
lndscp
save_name <- file.path(figure_dir, paste0(fit_ags, "vacc_anc_gmt"))
plot_single_landscape_panel(lndscp, label = "", save_name = save_name, delete_html = FALSE)
source("~/Documents/smith/labbook/roessler_netzl_et_al2023/code/ablandscape_fit_idvl.R")
lndscp <-r3js(
lndscp_3js,
rotation = c(-1.5836, 0.0100, -0.0131),
zoom = angle$zoom
)
lndsp
lndscp
vacc_groups
srg
# plot landscapes
for(srg in 1:length(unique(titertables_groups$sr_group))){
target_rows <- srg
lndscp_fits_t <- lndscp_fits[target_rows]
titertables_groups_t <- titertables_groups[target_rows,]
# plot idvl landscapes
lndscp_fits_idvl <- individual_lndscp_fits[[target_rows]]
lndscp_colors_idvl <- individual_sr_colors[[target_rows]]
data3js_idvl <- plot_idvl_landscapes_from_list(data3js, lndscp_fits_idvl, lndscp_colors_idvl)
lndscp_3js <- plot_landscapes_from_list(data3js_idvl, titertables_groups_t, lndscp_fits_t, map, gmt_data, agNames(map), agNames(map), lndscp_colors = sr_colors)
lndscp <-r3js(
lndscp_3js,
rotation = angle$rotation,
zoom = angle$zoom
)
if(unique(titertables_groups$sr_group)[srg] %in% vacc_groups){
lndscp <-r3js(
lndscp_3js,
rotation = c(-1.5836, 0.0100, -0.0131),
zoom = angle$zoom
)
}
srg_n <- titertables_groups$sr_group[target_rows]
srg_n <- gsub("/", "_", srg_n)
srg_n <- gsub(" ", "", srg_n)
save_name <- file.path(figure_dir, paste0(srg_n, "idvl_gmt_landscapes"))
plot_single_landscape_panel(lndscp, label = "", save_name = save_name, delete_html = FALSE)
}
source("~/Documents/smith/labbook/roessler_netzl_et_al2023/code/ablandscape_fit_idvl.R")
lndscp
lndscp <-r3js(
lndscp_3js,
rotation = c(-1.5836, 0.0100, -0.0131),
zoom = 1.7
)
lndscp
lndscp <-r3js(
lndscp_3js,
rotation = c(-1.5836, 0.0100, -0.0131),
zoom = 2
)
lndscp
# plot landscapes
for(srg in 1:length(unique(titertables_groups$sr_group))){
target_rows <- srg
lndscp_fits_t <- lndscp_fits[target_rows]
titertables_groups_t <- titertables_groups[target_rows,]
# plot idvl landscapes
lndscp_fits_idvl <- individual_lndscp_fits[[target_rows]]
lndscp_colors_idvl <- individual_sr_colors[[target_rows]]
data3js_idvl <- plot_idvl_landscapes_from_list(data3js, lndscp_fits_idvl, lndscp_colors_idvl)
lndscp_3js <- plot_landscapes_from_list(data3js_idvl, titertables_groups_t, lndscp_fits_t, map, gmt_data, agNames(map), agNames(map), lndscp_colors = sr_colors)
lndscp <-r3js(
lndscp_3js,
rotation = angle$rotation,
zoom = angle$zoom
)
if(unique(titertables_groups$sr_group)[srg] %in% vacc_groups){
lndscp <-r3js(
lndscp_3js,
rotation = c(-1.5836, 0.0100, -0.0131),
zoom = 2
)
}
srg_n <- titertables_groups$sr_group[target_rows]
srg_n <- gsub("/", "_", srg_n)
srg_n <- gsub(" ", "", srg_n)
save_name <- file.path(figure_dir, paste0(srg_n, "idvl_gmt_landscapes"))
plot_single_landscape_panel(lndscp, label = "", save_name = save_name, delete_html = FALSE)
}
source("~/Documents/smith/labbook/roessler_netzl_et_al2023/code/ablandscape_fit_multi.R")
lndscp
rm(list = ls())
library(Racmacs)
library(tidyverse)
library(patchwork)
library(titertools)
fc_df <- read.csv("som/titer_fold_changes/230412_titertools_fold_changes_3_ags.csv")
View(fc_df)
#----------- start fold change calculation
map <- read.acmap("data/maps/map-OmicronI+II+III-thresholded-full-P1m1.ace")
data_long <- long_map_info(map)
data_long %>%
filter(titer != "*") %>%
group_by(ag_name, sr_group) %>%
summarize(nr_sera = length(unique(sr_name))) %>%
pivot_wider(names_from = sr_group, values_from = nr_sera) -> nr_sera_table
# define titerplot function
source("functions/long_map_info.R")
source("functions/titer_lineplot_functions.R")
#----------- start fold change calculation
map <- read.acmap("data/maps/map-OmicronI+II+III-thresholded-full-P1m1.ace")
data_long <- long_map_info(map)
data_long %>%
filter(titer != "*") %>%
group_by(ag_name, sr_group) %>%
summarize(nr_sera = length(unique(sr_name))) %>%
pivot_wider(names_from = sr_group, values_from = nr_sera) -> nr_sera_table
View(nr_sera_table)
data_long %>%
filter(ag_name == "D614G") %>%
filter(titer != "*") %>%
group_by(ag_name, sr_group) %>%
summarize(nr_sera = length(unique(sr_name))) %>%
pivot_wider(names_from = sr_group, values_from = nr_sera) -> nr_sera_table
View(nr_sera_table)
print(nr_sera_table)
print(t(nr_sera_table))
4*21