Commit b8f7e2e2 authored by Carine Rey's avatar Carine Rey
Browse files

add auc in output but still some pbs with identical

parent ef8b0a4b
...@@ -11,3 +11,6 @@ RUN apt-get update && \ ...@@ -11,3 +11,6 @@ RUN apt-get update && \
RUN echo 'source("https://bioconductor.org/biocLite.R"); biocLite("ggtree")' > /tmp/packages.R \ RUN echo 'source("https://bioconductor.org/biocLite.R"); biocLite("ggtree")' > /tmp/packages.R \
&& Rscript /tmp/packages.R && Rscript /tmp/packages.R
RUN echo 'install.packages("flux")' > /tmp/packages.R \
&& Rscript /tmp/packages.R
...@@ -4,7 +4,7 @@ set -e ...@@ -4,7 +4,7 @@ set -e
IMAGE_NAME=r_basics IMAGE_NAME=r_basics
DOCKERFILE_DIR=. DOCKERFILE_DIR=.
TAG=08012018 TAG=09072018
REPO=carinerey/$IMAGE_NAME:$TAG REPO=carinerey/$IMAGE_NAME:$TAG
docker build -t $REPO -f ./Dockerfile $DOCKERFILE_DIR docker build -t $REPO -f ./Dockerfile $DOCKERFILE_DIR
......
...@@ -8,7 +8,7 @@ let env_tdg09 = docker_image ~account:"carinerey" ~name:"tdg09_python" ~tag:"v1. ...@@ -8,7 +8,7 @@ let env_tdg09 = docker_image ~account:"carinerey" ~name:"tdg09_python" ~tag:"v1.
let env_py = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" () let env_py = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" ()
let env_r = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"08012018" () let env_r = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"09072018" ()
let env_phyml = docker_image ~account:"carinerey" ~name:"phyml" ~tag:"v3.1" () let env_phyml = docker_image ~account:"carinerey" ~name:"phyml" ~tag:"v3.1" ()
......
...@@ -340,8 +340,8 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice ...@@ -340,8 +340,8 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let haPC_NeG5_indel_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_0.33_i" ) in let haPC_NeG5_indel_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_0.33_i" ) in
match (ha_PCOC_res) with match (h0_NeG1_res) with
| ( Some ha_PCOC) -> | ( Some h0_NeG1) ->
let t_choices_dir = make_t_choices_per_couple ~tree_prefix {ha_PCOC_res; let t_choices_dir = make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
h0_NeG1_res; h0_NeG2_res; h0_NeG3_res; h0_NeG4_res; h0_NeG5_res; h0_NeG1_res; h0_NeG2_res; h0_NeG3_res; h0_NeG4_res; h0_NeG5_res;
haPC_NeG1_res; haPC_NeG2_res;haPC_NeG3_res; haPC_NeG4_res; haPC_NeG5_res; haPC_NeG1_res; haPC_NeG2_res;haPC_NeG3_res; haPC_NeG4_res; haPC_NeG5_res;
...@@ -357,7 +357,7 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice ...@@ -357,7 +357,7 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let t_choices_condensed_plot_png = t_choices_dir / selector ["out_condensed.png"] in let t_choices_condensed_plot_png = t_choices_dir / selector ["out_condensed.png"] in
let rp_plot = t_choices_dir / selector ["out_condensed.recall_precision_ok.pdf"] in let rp_plot = t_choices_dir / selector ["out_condensed.recall_precision_ok.pdf"] in
let auc_tsv = t_choices_dir / selector ["out.auc_condensed.tsv"] in let auc_tsv = t_choices_dir / selector ["out.auc_condensed.tsv"] in
let tree_prefix = ha_PCOC.tree_prefix in let tree_prefix = h0_NeG1.tree_prefix in
Some {t_choices_max; t_choices_recall09; t_choices_complete ; t_choices_plot; t_choices_condensed_plot;t_choices_condensed_plot_png;rp_plot; auc_tsv; tree_prefix} Some {t_choices_max; t_choices_recall09; t_choices_complete ; t_choices_plot; t_choices_condensed_plot;t_choices_condensed_plot_png;rp_plot; auc_tsv; tree_prefix}
| _ -> None | _ -> None
......
...@@ -174,8 +174,8 @@ df_d = rbind.data.frame( ...@@ -174,8 +174,8 @@ df_d = rbind.data.frame(
df_d_H0H0_NeG5NeG5_NeC1, df_d_H0H0_NeG5NeG5_NeC1,
df_d_H0HaPC_NeG4_NeC_1, df_d_H0HaPC_NeG4_NeC_1,
df_d_H0HaPC_NeG1_NeC_4, df_d_H0HaPC_NeG1_NeC_4,
df_d_H0H0_NeG4NeG4_NeC2, df_d_H0H0_NeG4NeG4_NeC1,
df_d_H0H0_NeG2NeG2_NeC4, df_d_H0H0_NeG1NeG1_NeC4,
df_d_H0HaPC_NeG5_indel df_d_H0HaPC_NeG5_indel
) )
...@@ -366,9 +366,10 @@ df_auc = do.call(rbind, lapply(split(df_out,paste0(df_out$methode,df_out$couple) ...@@ -366,9 +366,10 @@ df_auc = do.call(rbind, lapply(split(df_out,paste0(df_out$methode,df_out$couple)
P = x$precision98_02 P = x$precision98_02
R = R[! is.na(P)] R = R[! is.na(P)]
P = P[! is.na(P)] P = P[! is.na(P)]
print(R) auc = 0
print(P) if (length(P) > 1) {
auc = auc(x = R, y = P, dens = 0) auc = auc(x = R, y = P, dens = 1)
}
df= data.frame(methode =x$methode[1] ,couple =x$couple[1] ,auc=auc) df= data.frame(methode =x$methode[1] ,couple =x$couple[1] ,auc=auc)
return(df) return(df)
})) }))
...@@ -499,7 +500,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi ...@@ -499,7 +500,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
plot = plot + theme(axis.text.x = element_text(angle = 45, hjust = 1)) plot = plot + theme(axis.text.x = element_text(angle = 45, hjust = 1))
plot} plot}
plot = plot_PR_c(c("H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG4","H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG1/NeG1_NeC_4", "H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4") plot = plot_PR_c(c("H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG4","H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG1/NeG1_NeC_4", "H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4"))
plot1 = plot_PR_c(c("H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG4")) plot1 = plot_PR_c(c("H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG4"))
plot2 = plot_PR_c(c("H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG1/NeG1_NeC_4","NULL")) plot2 = plot_PR_c(c("H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG1/NeG1_NeC_4","NULL"))
plot3 = plot_PR_c(c("H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4","NULL")) plot3 = plot_PR_c(c("H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4","NULL"))
......
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