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
# 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
######################