From 343f867eed1c24a75f3ff0739cda6cfbd1fe8818 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Thu, 2 Sep 2021 17:40:24 +0100
Subject: [PATCH] saving work for the day

---
 dynamut/split_csv.sh           | 4 +++-
 scripts/functions/lf_bp.R      | 8 +++++---
 scripts/functions/test_lf_bp.R | 9 ++++++---
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/dynamut/split_csv.sh b/dynamut/split_csv.sh
index b5f15f1..18103c6 100755
--- a/dynamut/split_csv.sh
+++ b/dynamut/split_csv.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# FIXME: This is written for expediency to kickstart running dynamut and mcsm-NA
+# FIXME: This is written for expediency to kickstart running dynamut, mcsm-PPI2 (batch pf 50) and mCSM-NA (batch of 20)
 
 # Usage: ~/git/LSHTM_analysis/dynamut/split_csv.sh <input file> <output dir> <chunk size in lines>
 # copy your snp file to split into the dynamut dir
@@ -13,7 +13,9 @@ mkdir -p ${OUTDIR}/${CHUNK}
 cd ${OUTDIR}/${CHUNK}
 
 split ../../${INFILE} -l ${CHUNK} -d snp_batch_
+#split ${INFILE} -l ${CHUNK} -d snp_batch_
 
 # use case
 #~/git/LSHTM_analysis/dynamut/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50
 #~/git/LSHTM_analysis/dynamut/split_csv.sh embb_mcsm_formatted_snps.csv snp_batches 50
+~/git/LSHTM_analysis/dynamut/split_csv.sh pnca_mcsm_formatted_snps.csv snp_batches 50
diff --git a/scripts/functions/lf_bp.R b/scripts/functions/lf_bp.R
index 4677548..608247d 100644
--- a/scripts/functions/lf_bp.R
+++ b/scripts/functions/lf_bp.R
@@ -24,7 +24,7 @@ lf_bp <- function(lf_df
                   , my_pts = 22 # plot title size)
                   , make_boxplot = FALSE
                   , bp_width = c("auto", 0.5)
-                  , add_stats = FALSE
+                  , add_stats = TRUE
                   , stat_grp_comp = c("DM", "OM")
                   , stat_method = "wilcox.test"
                   , my_paired = FALSE
@@ -104,8 +104,10 @@ lf_bp <- function(lf_df
     OutPlot = OutPlot + stat_compare_means(comparisons = my_comparisonsL
                        , method = stat_method
                        , paired = my_paired
-                       , label = stat_label[1])
-    } 
+                       , label = stat_label[2])
+    return(OutPlot)
+    }
+   
    return(OutPlot)
 }
 
diff --git a/scripts/functions/test_lf_bp.R b/scripts/functions/test_lf_bp.R
index 42b78bf..f3d2327 100644
--- a/scripts/functions/test_lf_bp.R
+++ b/scripts/functions/test_lf_bp.R
@@ -12,9 +12,9 @@ source("../functions/lf_bp.R")
 ######################
 # Make plot: ggplot
 ######################
-lf_bp(lf_df = lf_dynamut2
-      , p_title = "Dynamut2"
-      , colour_categ = "ddg_dynamut2_outcome"
+lf_bp(lf_df = lf_encomddg
+      , p_title = "ENCoM-DDG"
+      , colour_categ = "ddg_encom_outcome"
       , x_grp = "mutation_info"
       , y_var = "param_value"
       , facet_var = "param_type"
@@ -36,6 +36,9 @@ lf_bp(lf_df = lf_dynamut2
       , my_paired = FALSE
       , stat_label = c("p.format", "p.signif") )
 
+#wilcox.test(wf_encomdds$`EnCOM ΔΔS`[wf_encomdds$mutation_info == "DM"]
+#            , wf_encomdds$`EnCOM ΔΔS`[wf_encomdds$mutation_info == "OM"])
+
 ######################
 # Make plot: plotly
 ######################