Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

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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