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saving work for the day

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This commit is contained in:
Tanushree Tunstall 2021-09-02 17:40:24 +01:00
parent a981580b7a
commit 605eb54526
3 changed files with 14 additions and 7 deletions
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4
dynamut/split_csv.sh
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@ -1,6 +1,6 @@
#!/bin/bash #!/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> # 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 # copy your snp file to split into the dynamut dir
@ -13,7 +13,9 @@ mkdir -p ${OUTDIR}/${CHUNK}
cd ${OUTDIR}/${CHUNK} cd ${OUTDIR}/${CHUNK}
split ../../${INFILE} -l ${CHUNK} -d snp_batch_ split ../../${INFILE} -l ${CHUNK} -d snp_batch_
#split ${INFILE} -l ${CHUNK} -d snp_batch_
# use case # use case
#~/git/LSHTM_analysis/dynamut/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50 #~/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 embb_mcsm_formatted_snps.csv snp_batches 50
~/git/LSHTM_analysis/dynamut/split_csv.sh pnca_mcsm_formatted_snps.csv snp_batches 50

8
scripts/functions/lf_bp.R
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@ -24,7 +24,7 @@ lf_bp <- function(lf_df
, my_pts = 22 # plot title size) , my_pts = 22 # plot title size)
, make_boxplot = FALSE , make_boxplot = FALSE
, bp_width = c("auto", 0.5) , bp_width = c("auto", 0.5)
, add_stats = FALSE , add_stats = TRUE
, stat_grp_comp = c("DM", "OM") , stat_grp_comp = c("DM", "OM")
, stat_method = "wilcox.test" , stat_method = "wilcox.test"
, my_paired = FALSE , my_paired = FALSE
@ -104,8 +104,10 @@ lf_bp <- function(lf_df
OutPlot = OutPlot + stat_compare_means(comparisons = my_comparisonsL OutPlot = OutPlot + stat_compare_means(comparisons = my_comparisonsL
, method = stat_method , method = stat_method
, paired = my_paired , paired = my_paired
, label = stat_label[1]) , label = stat_label[2])
} return(OutPlot)
}
return(OutPlot) return(OutPlot)
} }

9
scripts/functions/test_lf_bp.R
View file

@ -12,9 +12,9 @@ source("../functions/lf_bp.R")
###################### ######################
# Make plot: ggplot # Make plot: ggplot
###################### ######################
lf_bp(lf_df = lf_dynamut2 lf_bp(lf_df = lf_encomddg
, p_title = "Dynamut2" , p_title = "ENCoM-DDG"
, colour_categ = "ddg_dynamut2_outcome" , colour_categ = "ddg_encom_outcome"
, x_grp = "mutation_info" , x_grp = "mutation_info"
, y_var = "param_value" , y_var = "param_value"
, facet_var = "param_type" , facet_var = "param_type"
@ -36,6 +36,9 @@ lf_bp(lf_df = lf_dynamut2
, my_paired = FALSE , my_paired = FALSE
, stat_label = c("p.format", "p.signif") ) , 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 # Make plot: plotly
###################### ######################