vignettes/graphes_JASA.R
In Marie-PerrotDockes/sanssouci.hmm: Confindence bound on the FDP after post-selection under an HMM
get_res <- function(name){
# l <- load(paste0(name, ".RData"))
# Result <- get(l)
# res<- Result %>%
# # get_results()
# mise_en_forme()
# save(res, file = paste0("res_",name, ".Rdata"))
# res
}
plot_sim <- function(name, type="sel"){
l <- load(paste0("res_",name, ".Rdata"))
res <- get(l)
res <- res %>%
filter(as.numeric(Nom)!=8)
# col1 <- viridis_pal()(9)
cols <- pal_nejm()(8)
col1 <- c(cols[1:2],c("chocolate1","chocolate2","chocolate3"),
cols[c(4,7,5)])
sel <- c(1,2,7,8)
lab_high <- c(
"Naive",
"Oracle",
"Plug-in" ,
"Boot1 0.9",
"Boot1 0.5",
"Boot1 0.1",
"Boot2",
"Boot3")
ord_high <- c(
"V_HMM_boot_naif",
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot_qdelta",
"V_HMM_boot_qdemi",
"V_HMM_boot_q1_moins_delta",
"V_HMM_boot_samesel",
"V_HMM_boot3")
if(type!="sel"){
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col1, labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
} else{
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high[sel]), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col1[sel], labels = rev(lab_high[sel])) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
}
ggsave(p1, file =paste0(name,"_diff.pdf"), device =cairo_pdf, width= 16, height =4)
## graphe de puissance :
p2 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graphe_puiss_mean(order = rev(ord_high[sel])) +
scale_color_manual(values = col1[sel], labels = rev(lab_high[sel])) +
theme(legend.text = element_text(size=14))
ggsave(p2, file =paste0(name,"puiss_mean.pdf"), device =cairo_pdf, width= 16, height =4)
lab_low <- c( "Naive",
"Oracle",
"Boot2",
"Boot3")
ord_low <- c(
"V_HMM_small_boot_naif",
"V_HMM_small_or",
"V_HMM_small_boot_samesel",
"V_HMM_small_boot3")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
# mutate(Size = as.character(Size)) %>%
# mutate_if(is.numeric, ~./as.numeric(Size)) %>%
graph_diff_high_FDR(order = rev(ord_low),
row_wrap =1, num_1 = 0.07,
num_2 = 0.07, type ="low") +
# scale_color_manual(labels = rev(lab_low[-1]), values = col1) +
scale_color_manual(values = col1[sel],labels = rev(lab_low)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
ggsave(p1, file =paste0(name, "_lower_diff",".pdf"), device =cairo_pdf, width= 16, height =4)
IC <-res %>%
select( - V_HMM_est_aldemi ) %>%
bx_plot_prop(num_sim =3, col1 = rev(col1[sel[-4]]))+
scale_color_manual(values = rev(col1[sel[-4]]),labels = lab_low[-1]) +
theme(legend.text = element_text(size=14),legend.title = element_blank())+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))+
scale_shape_manual(values = c(2, 4), labels = c("FDR estimate", "Actual FDP"))
ggsave(IC, file =paste0(name, "_IC",".pdf"), device =cairo_pdf, width= 16, height =4)
# return(res)
}
Res <- get_res("res_simu_delta")
plot_sim("res_simu_delta", type ="all")
## avec H0 knowledge
Res <- get_res("res_simu_delta_h0")
plot_sim("res_simu_delta_h0")
## unknown f0 :
res_uf0 <- get_res("delta_highdet_m3200_uf0")
plot_sim("delta_highdet_m3200_uf0")
#
# res_ff0 <- get_res("delta_highdet_uf0_start_falsef0_m3200")
#
# plot_sim("delta_highdet_uf0_start_falsef0_m3200")
Res <- get_res("delta_highdet_uf0_start_locfdr_m3200")
plot_sim("delta_highdet_uf0_start_locfdr_m3200")
##
## graphe realiste
## graphe avec les determinants :
# res_realiste<- get_res("Realist_frac1")
#
# plot_sim("Realist_frac1")
#
Res <- get_res("delta_diffdet_m3200")
cols <- pal_nejm()(8)
col1 <- c(cols[1:2],c("chocolate1","chocolate2","chocolate3"),
cols[c(4,7,5)])
lab_high_tot <- c(
"Naive",
"Oracle",
"Plug-in" ,
"Boot1 0.9",
"Boot1 0.5",
"Boot1 0.1",
"Boot2",
"Boot3")
ord_high_tot <- c(
"V_HMM_boot_naif",
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot_qdelta",
"V_HMM_boot_qdemi",
"V_HMM_boot_q1_moins_delta",
"V_HMM_boot_samesel",
"V_HMM_boot3")
l <- load(paste0("res_delta_diffdet_m3200.Rdata"))
res <- get(l)
sel <- c(1,2,7,8)
res %>%
mutate(Det_A = map_dbl(A, ~round(det(.),2))) %>%
filter(Det_A==0) %>%
mutate(Diff= V_real -V_HMM_boot_qdemi) %>%
pull(Diff) %>% quantile(probs = seq(0,1,0.1),na.rm=TRUE)
lab_high <- c("Simes",lab_high_tot[sel])
ord_high <- c("V_simes",
ord_high_tot[sel])
p1 <- res %>%
mutate(Det_A = map_chr(A, ~paste("Det(A) ==",round(det(.),2)))) %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR_facet(order = rev(ord_high),
row_wrap =1, var_comp ="Det_A") +
scale_color_manual(labels = rev(lab_high), values = c(col1[sel],"grey50")) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
ggsave(p1, file =paste0("delta_diffdet_m3200_diff.pdf"),
device =cairo_pdf, width= 16, height =12)
# return(res)
res_realiste<- get_res("Realist_frac1")
res_realiste_otherfrac<- get_res("Realist_other_frac_delta")
load("res_Realist_other_frac_delta.Rdata")
res_realiste_otherfrac<-res
load("res_Realist_frac1.Rdata")
sel <- c(1,7,8)
sel_col <-c(1,2,8)
res_reali <- rbind(res, res_realiste_otherfrac)
lab_high <- c( "Simes",lab_high_tot[sel])
ord_high <- c("V_simes",ord_high_tot[sel])
p1 <- res_reali %>%
filter(!(as.numeric(Nom)%in% c(2,8))) %>%
mutate(Det_A = map_chr(tumorFraction, ~paste("Tf ==",.)),
Det_A = factor(Det_A,
levels = c("Tf == 1", "Tf == 0.7","Tf == 0.5","Tf == 0.3") )) %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR_facet(order = rev(ord_high),
row_wrap =1, var_comp ="Det_A") +
scale_color_manual(values = c(col1[sel_col], "grey50"), labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1))) +
scale_y_continuous(breaks = c(0,0.2,0.5,0.7,1))
ggsave(p1, file =paste0("reali_m10000_diff.pdf"),
device =cairo_pdf, width= 10, height =6)
## puissance
p1 <- res_reali %>%
filter(!(as.numeric(Nom)%in% c(2,8))) %>%
mutate(Det_A = map_chr(tumorFraction, ~paste("Tf ==",.)),
Det_A = factor(Det_A,
levels = c("Tf == 1", "Tf == 0.7","Tf == 0.5","Tf == 0.3") )) %>%
select( - V_HMM_est_aldemi ) %>%
graphe_puiss_mean_facet(order = rev(ord_high), var_comp ="Det_A") +
scale_color_manual(values = c(col1[sel_col], "grey50"), labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=1, alpha =1))) +
scale_y_continuous(breaks = c(0,0.2,0.5,0.7,1))
ggsave(p1, file =paste0("reali_m10000_puiss.pdf"),
device =cairo_pdf, width= 10, height =6)
## Ajout BNR et Bram :
load("~/posthoc/HMM/articleMarie/JASA/Simu_papier_marie/Res_simu_other.RData")
name <- "res_simu_delta"
l <- load(paste0("res_",name, ".Rdata"))
res <- get(l) %>%
filter(as.numeric(Nom)!=8)
res2 <- Res_simu_other %>% mutate( Nom = case_when(
Nom == "pval_tresh" ~ "bgroup('{',p < 0.05,'}')",
Nom == "pvalm_sel" ~ "bgroup('{',p < 0.05,'}')~intersect()~bgroup('{','1, ..., 200' ,'}')",
Nom == "sel_viter_est" ~ "Viterbi",
Nom == "sel_viter_min_size" ~ "Viterbi + 4",
Nom == "pvalm_tresh_H0" ~ "H0~intersect()~ bgroup('{',p < 0.05 ,'}')",
Nom == "sel_viter_est_H0" ~ "H0~intersect()~Viterbi",
Nom == "H1" ~ "H1",
Nom == "pval_lfdr" ~ "bgroup('{',p < th,'}')",
Nom == "lfdr_tresh" ~ "SC(0.05)",
Nom == "sel_idpval" ~ "SC(FDR[p])",
Nom == "lfdr_tresh_viter" ~ "SC(FDR[v])",
Nom == "block" ~ "bgroup('{','1, ..., 200' ,'}')"
),
Nom = factor(
Nom,
levels = c(
"bgroup('{',p < 0.05,'}')",
"bgroup('{',p < 0.05,'}')~intersect()~bgroup('{','1, ..., 200' ,'}')",
"SC(FDR[p])",
"SC(0.05)",
"bgroup('{',p < th,'}')",
"Viterbi",
"SC(FDR[v])",
"Viterbi + 4",
"bgroup('{','1, ..., 200' ,'}')",
"H1",
"H0~intersect()~ bgroup('{',p < 0.05 ,'}')",
"H0~intersect()~Viterbi"
)
)) %>%
filter(as.numeric(Nom)!=8)
res <- res %>% mutate(Nom = as.character(Nom)) %>% left_join(res2)
# col1 <- viridis_pal()(9)
cols <- pal_nejm()(8)
col1 <- c(rep("grey",3),"grey20", cols[1:2],c("chocolate1","chocolate2","chocolate3"),
cols[c(4,7,5)])
sel <- c(1,2,7,8)
lab_high <- c(
"Naive",
"Oracle",
"Plug-in" ,
"Boot1 0.9",
"Boot1 0.5",
"Boot1 0.1",
"Boot2",
"Boot3",
"Katsevitch, Ramdas ",
"BNR m",
"BNR 2m1","Simes")
ord_high <- c(
"V_HMM_boot_naif",
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot_qdelta",
"V_HMM_boot_qdemi",
"V_HMM_boot_q1_moins_delta",
"V_HMM_boot_samesel",
"V_HMM_boot3",
"V_bram",
"V_bnr_m",
"V_bnr_2m1", "V_simes")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col1, labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
p1
ggsave(p1, file =paste0("compare_BNR_ramdas_diff_all.pdf"), device =cairo_pdf, width= 16, height =4)
## graphe pour introduction :
library(ggthemes)
col_intro <- c( few_pal()(4),"grey20",col1[c(5,10,11)])
lab_high <- c(
"Oracle",
"Plug-in" ,
"Boot3",
"KR",
"BNR m",
"DBNR",
"DBNR_tree",
"Simes")
ord_high <- c(
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot3",
"V_bram",
"V_bnr_m",
"V_DBNR_part",
"V_DBNR_tree",
"V_simes")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col_intro, labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
p1
ggsave(p1, file =paste0("compare_intro.jpeg"),
width= 16, height =4)
col_intro <- c( few_pal()(4)[3:4],"grey20",col1[c(5,11)])
col_intro <- c("mediumblue", "slateblue2", "orchid3",col1[c(5,11)])
col_intro <- c("paleturquoise3", "palevioletred", "grey30",col1[c(5,10,11)])
lab_high <- c(
"Oracle",
"Plug-in",
"Boot3",
"KR",
"BNR","Simes")
ord_high <- c(
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot3",
"V_bram",
"V_bnr_m",
"V_simes")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col_intro, labels = rev(lab_high)) +
theme(text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
p1
ggsave(p1, file =paste0("compare_intro_ssdbnr.pdf"),device =cairo_pdf,
width= 13, height =3)
## en vrai je pense pas mettre simes et BNR
cols <- pal_nejm()(8)
col1 <- c("grey20", cols[1:2],c("chocolate1","chocolate2","chocolate3"),
cols[c(4,7,5)])
sel <- c(1,2,7,8)
lab_high <- c(
"Naive",
"Oracle",
"Plug-in" ,
"Boot1 0.9",
"Boot1 0.5",
"Boot1 0.1",
"Boot2",
"Boot3",
"KR")
ord_high <- c(
"V_HMM_boot_naif",
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot_qdelta",
"V_HMM_boot_qdemi",
"V_HMM_boot_q1_moins_delta",
"V_HMM_boot_samesel",
"V_HMM_boot3",
"V_bram")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col1, labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
p1
ggsave(p1, file =paste0("compare_BNR_ramdas_diff.pdf"), device =cairo_pdf, width= 16, height =4)
sel <- c(1,2,7,8,9)
p2 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graphe_puiss_mean(order = rev(ord_high[sel])) +
scale_color_manual(values = col1[sel], labels = rev(lab_high[sel])) +
theme(legend.text = element_text(size=14))
ggsave(p2, file =paste0("ramkats_puiss_mean.pdf"), device =cairo_pdf, width= 16, height =4)
##
Marie-PerrotDockes/sanssouci.hmm documentation built on Oct. 26, 2023, 10:36 a.m.
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get_res <- function(name){
# l <- load(paste0(name, ".RData"))
# Result <- get(l)
# res<- Result %>%
# # get_results()
# mise_en_forme()
# save(res, file = paste0("res_",name, ".Rdata"))
# res
}
plot_sim <- function(name, type="sel"){
l <- load(paste0("res_",name, ".Rdata"))
res <- get(l)
res <- res %>%
filter(as.numeric(Nom)!=8)
# col1 <- viridis_pal()(9)
cols <- pal_nejm()(8)
col1 <- c(cols[1:2],c("chocolate1","chocolate2","chocolate3"),
cols[c(4,7,5)])
sel <- c(1,2,7,8)
lab_high <- c(
"Naive",
"Oracle",
"Plug-in" ,
"Boot1 0.9",
"Boot1 0.5",
"Boot1 0.1",
"Boot2",
"Boot3")
ord_high <- c(
"V_HMM_boot_naif",
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot_qdelta",
"V_HMM_boot_qdemi",
"V_HMM_boot_q1_moins_delta",
"V_HMM_boot_samesel",
"V_HMM_boot3")
if(type!="sel"){
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col1, labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
} else{
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high[sel]), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col1[sel], labels = rev(lab_high[sel])) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
}
ggsave(p1, file =paste0(name,"_diff.pdf"), device =cairo_pdf, width= 16, height =4)
## graphe de puissance :
p2 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graphe_puiss_mean(order = rev(ord_high[sel])) +
scale_color_manual(values = col1[sel], labels = rev(lab_high[sel])) +
theme(legend.text = element_text(size=14))
ggsave(p2, file =paste0(name,"puiss_mean.pdf"), device =cairo_pdf, width= 16, height =4)
lab_low <- c( "Naive",
"Oracle",
"Boot2",
"Boot3")
ord_low <- c(
"V_HMM_small_boot_naif",
"V_HMM_small_or",
"V_HMM_small_boot_samesel",
"V_HMM_small_boot3")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
# mutate(Size = as.character(Size)) %>%
# mutate_if(is.numeric, ~./as.numeric(Size)) %>%
graph_diff_high_FDR(order = rev(ord_low),
row_wrap =1, num_1 = 0.07,
num_2 = 0.07, type ="low") +
# scale_color_manual(labels = rev(lab_low[-1]), values = col1) +
scale_color_manual(values = col1[sel],labels = rev(lab_low)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
ggsave(p1, file =paste0(name, "_lower_diff",".pdf"), device =cairo_pdf, width= 16, height =4)
IC <-res %>%
select( - V_HMM_est_aldemi ) %>%
bx_plot_prop(num_sim =3, col1 = rev(col1[sel[-4]]))+
scale_color_manual(values = rev(col1[sel[-4]]),labels = lab_low[-1]) +
theme(legend.text = element_text(size=14),legend.title = element_blank())+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))+
scale_shape_manual(values = c(2, 4), labels = c("FDR estimate", "Actual FDP"))
ggsave(IC, file =paste0(name, "_IC",".pdf"), device =cairo_pdf, width= 16, height =4)
# return(res)
}
Res <- get_res("res_simu_delta")
plot_sim("res_simu_delta", type ="all")
## avec H0 knowledge
Res <- get_res("res_simu_delta_h0")
plot_sim("res_simu_delta_h0")
## unknown f0 :
res_uf0 <- get_res("delta_highdet_m3200_uf0")
plot_sim("delta_highdet_m3200_uf0")
#
# res_ff0 <- get_res("delta_highdet_uf0_start_falsef0_m3200")
#
# plot_sim("delta_highdet_uf0_start_falsef0_m3200")
Res <- get_res("delta_highdet_uf0_start_locfdr_m3200")
plot_sim("delta_highdet_uf0_start_locfdr_m3200")
##
## graphe realiste
## graphe avec les determinants :
# res_realiste<- get_res("Realist_frac1")
#
# plot_sim("Realist_frac1")
#
Res <- get_res("delta_diffdet_m3200")
cols <- pal_nejm()(8)
col1 <- c(cols[1:2],c("chocolate1","chocolate2","chocolate3"),
cols[c(4,7,5)])
lab_high_tot <- c(
"Naive",
"Oracle",
"Plug-in" ,
"Boot1 0.9",
"Boot1 0.5",
"Boot1 0.1",
"Boot2",
"Boot3")
ord_high_tot <- c(
"V_HMM_boot_naif",
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot_qdelta",
"V_HMM_boot_qdemi",
"V_HMM_boot_q1_moins_delta",
"V_HMM_boot_samesel",
"V_HMM_boot3")
l <- load(paste0("res_delta_diffdet_m3200.Rdata"))
res <- get(l)
sel <- c(1,2,7,8)
res %>%
mutate(Det_A = map_dbl(A, ~round(det(.),2))) %>%
filter(Det_A==0) %>%
mutate(Diff= V_real -V_HMM_boot_qdemi) %>%
pull(Diff) %>% quantile(probs = seq(0,1,0.1),na.rm=TRUE)
lab_high <- c("Simes",lab_high_tot[sel])
ord_high <- c("V_simes",
ord_high_tot[sel])
p1 <- res %>%
mutate(Det_A = map_chr(A, ~paste("Det(A) ==",round(det(.),2)))) %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR_facet(order = rev(ord_high),
row_wrap =1, var_comp ="Det_A") +
scale_color_manual(labels = rev(lab_high), values = c(col1[sel],"grey50")) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
ggsave(p1, file =paste0("delta_diffdet_m3200_diff.pdf"),
device =cairo_pdf, width= 16, height =12)
# return(res)
res_realiste<- get_res("Realist_frac1")
res_realiste_otherfrac<- get_res("Realist_other_frac_delta")
load("res_Realist_other_frac_delta.Rdata")
res_realiste_otherfrac<-res
load("res_Realist_frac1.Rdata")
sel <- c(1,7,8)
sel_col <-c(1,2,8)
res_reali <- rbind(res, res_realiste_otherfrac)
lab_high <- c( "Simes",lab_high_tot[sel])
ord_high <- c("V_simes",ord_high_tot[sel])
p1 <- res_reali %>%
filter(!(as.numeric(Nom)%in% c(2,8))) %>%
mutate(Det_A = map_chr(tumorFraction, ~paste("Tf ==",.)),
Det_A = factor(Det_A,
levels = c("Tf == 1", "Tf == 0.7","Tf == 0.5","Tf == 0.3") )) %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR_facet(order = rev(ord_high),
row_wrap =1, var_comp ="Det_A") +
scale_color_manual(values = c(col1[sel_col], "grey50"), labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1))) +
scale_y_continuous(breaks = c(0,0.2,0.5,0.7,1))
ggsave(p1, file =paste0("reali_m10000_diff.pdf"),
device =cairo_pdf, width= 10, height =6)
## puissance
p1 <- res_reali %>%
filter(!(as.numeric(Nom)%in% c(2,8))) %>%
mutate(Det_A = map_chr(tumorFraction, ~paste("Tf ==",.)),
Det_A = factor(Det_A,
levels = c("Tf == 1", "Tf == 0.7","Tf == 0.5","Tf == 0.3") )) %>%
select( - V_HMM_est_aldemi ) %>%
graphe_puiss_mean_facet(order = rev(ord_high), var_comp ="Det_A") +
scale_color_manual(values = c(col1[sel_col], "grey50"), labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=1, alpha =1))) +
scale_y_continuous(breaks = c(0,0.2,0.5,0.7,1))
ggsave(p1, file =paste0("reali_m10000_puiss.pdf"),
device =cairo_pdf, width= 10, height =6)
## Ajout BNR et Bram :
load("~/posthoc/HMM/articleMarie/JASA/Simu_papier_marie/Res_simu_other.RData")
name <- "res_simu_delta"
l <- load(paste0("res_",name, ".Rdata"))
res <- get(l) %>%
filter(as.numeric(Nom)!=8)
res2 <- Res_simu_other %>% mutate( Nom = case_when(
Nom == "pval_tresh" ~ "bgroup('{',p < 0.05,'}')",
Nom == "pvalm_sel" ~ "bgroup('{',p < 0.05,'}')~intersect()~bgroup('{','1, ..., 200' ,'}')",
Nom == "sel_viter_est" ~ "Viterbi",
Nom == "sel_viter_min_size" ~ "Viterbi + 4",
Nom == "pvalm_tresh_H0" ~ "H0~intersect()~ bgroup('{',p < 0.05 ,'}')",
Nom == "sel_viter_est_H0" ~ "H0~intersect()~Viterbi",
Nom == "H1" ~ "H1",
Nom == "pval_lfdr" ~ "bgroup('{',p < th,'}')",
Nom == "lfdr_tresh" ~ "SC(0.05)",
Nom == "sel_idpval" ~ "SC(FDR[p])",
Nom == "lfdr_tresh_viter" ~ "SC(FDR[v])",
Nom == "block" ~ "bgroup('{','1, ..., 200' ,'}')"
),
Nom = factor(
Nom,
levels = c(
"bgroup('{',p < 0.05,'}')",
"bgroup('{',p < 0.05,'}')~intersect()~bgroup('{','1, ..., 200' ,'}')",
"SC(FDR[p])",
"SC(0.05)",
"bgroup('{',p < th,'}')",
"Viterbi",
"SC(FDR[v])",
"Viterbi + 4",
"bgroup('{','1, ..., 200' ,'}')",
"H1",
"H0~intersect()~ bgroup('{',p < 0.05 ,'}')",
"H0~intersect()~Viterbi"
)
)) %>%
filter(as.numeric(Nom)!=8)
res <- res %>% mutate(Nom = as.character(Nom)) %>% left_join(res2)
# col1 <- viridis_pal()(9)
cols <- pal_nejm()(8)
col1 <- c(rep("grey",3),"grey20", cols[1:2],c("chocolate1","chocolate2","chocolate3"),
cols[c(4,7,5)])
sel <- c(1,2,7,8)
lab_high <- c(
"Naive",
"Oracle",
"Plug-in" ,
"Boot1 0.9",
"Boot1 0.5",
"Boot1 0.1",
"Boot2",
"Boot3",
"Katsevitch, Ramdas ",
"BNR m",
"BNR 2m1","Simes")
ord_high <- c(
"V_HMM_boot_naif",
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot_qdelta",
"V_HMM_boot_qdemi",
"V_HMM_boot_q1_moins_delta",
"V_HMM_boot_samesel",
"V_HMM_boot3",
"V_bram",
"V_bnr_m",
"V_bnr_2m1", "V_simes")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col1, labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
p1
ggsave(p1, file =paste0("compare_BNR_ramdas_diff_all.pdf"), device =cairo_pdf, width= 16, height =4)
## graphe pour introduction :
library(ggthemes)
col_intro <- c( few_pal()(4),"grey20",col1[c(5,10,11)])
lab_high <- c(
"Oracle",
"Plug-in" ,
"Boot3",
"KR",
"BNR m",
"DBNR",
"DBNR_tree",
"Simes")
ord_high <- c(
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot3",
"V_bram",
"V_bnr_m",
"V_DBNR_part",
"V_DBNR_tree",
"V_simes")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col_intro, labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
p1
ggsave(p1, file =paste0("compare_intro.jpeg"),
width= 16, height =4)
col_intro <- c( few_pal()(4)[3:4],"grey20",col1[c(5,11)])
col_intro <- c("mediumblue", "slateblue2", "orchid3",col1[c(5,11)])
col_intro <- c("paleturquoise3", "palevioletred", "grey30",col1[c(5,10,11)])
lab_high <- c(
"Oracle",
"Plug-in",
"Boot3",
"KR",
"BNR","Simes")
ord_high <- c(
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot3",
"V_bram",
"V_bnr_m",
"V_simes")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col_intro, labels = rev(lab_high)) +
theme(text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
p1
ggsave(p1, file =paste0("compare_intro_ssdbnr.pdf"),device =cairo_pdf,
width= 13, height =3)
## en vrai je pense pas mettre simes et BNR
cols <- pal_nejm()(8)
col1 <- c("grey20", cols[1:2],c("chocolate1","chocolate2","chocolate3"),
cols[c(4,7,5)])
sel <- c(1,2,7,8)
lab_high <- c(
"Naive",
"Oracle",
"Plug-in" ,
"Boot1 0.9",
"Boot1 0.5",
"Boot1 0.1",
"Boot2",
"Boot3",
"KR")
ord_high <- c(
"V_HMM_boot_naif",
"V_HMM_or",
"V_HMM_est",
"V_HMM_boot_qdelta",
"V_HMM_boot_qdemi",
"V_HMM_boot_q1_moins_delta",
"V_HMM_boot_samesel",
"V_HMM_boot3",
"V_bram")
p1 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graph_diff_high_FDR(order = rev(ord_high), row_wrap =1,
num_1 = 0.1, num_2 =0.1) +
scale_color_manual(values = col1, labels = rev(lab_high)) +
theme(legend.text = element_text(size=14))+
guides(color=guide_legend(override.aes = list(size=3, alpha =1)))
p1
ggsave(p1, file =paste0("compare_BNR_ramdas_diff.pdf"), device =cairo_pdf, width= 16, height =4)
sel <- c(1,2,7,8,9)
p2 <- res %>%
select( - V_HMM_est_aldemi ) %>%
graphe_puiss_mean(order = rev(ord_high[sel])) +
scale_color_manual(values = col1[sel], labels = rev(lab_high[sel])) +
theme(legend.text = element_text(size=14))
ggsave(p2, file =paste0("ramkats_puiss_mean.pdf"), device =cairo_pdf, width= 16, height =4)
##
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