adde format_results_dynamut2.py and ran shiny scripts for barplots
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8cdf720702
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9 changed files with 235 additions and 59 deletions
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@ -23,7 +23,7 @@ my_df_u_lig = data.frame()
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dup_muts = data.frame()
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#===========================
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# Read file: struct params
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# Read file: struct params
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#===========================
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#df = read.csv(infile_params, header = T)
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@ -30,8 +30,12 @@ site_snp_count_bp <- function (plotdf
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, axis_text_size = 25
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, axis_label_size = 22
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, xaxis_title = "Number of nsSNPs"
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, yaxis_title = "Number of Sites"){
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, yaxis_title = "Number of Sites"
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, title_colour = "chocolate4"
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, subtitle_text = NULL
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, subtitle_size = 20
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, subtitle_colour = "pink")
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{
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# dim of plotdf
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cat(paste0("\noriginal df dimensions:"
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, "\nNo. of rows:", nrow(plotdf)
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@ -83,9 +87,9 @@ site_snp_count_bp <- function (plotdf
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# FIXME: should really be legend title
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# but atm being using as plot title
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my_leg_title = paste0("Total nsSNPs:", tot_muts
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, ", Total no. of nsSNPs sites:", tot_sites)
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bp_plot_title = my_leg_title
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#my_leg_title
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bp_plot_title = paste0("Total nsSNPs: ", tot_muts
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, ", Total no. of nsSNPs sites: ", tot_sites)
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#-------------
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# start plot 2
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@ -111,11 +115,16 @@ site_snp_count_bp <- function (plotdf
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#, legend.position = c(0.73,0.8)
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#, legend.text = element_text(size = leg_text_size)
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#, legend.title = element_text(size = axis_label_size)
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, plot.title = element_text(size = leg_text_size)) +
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, plot.title = element_text(size = leg_text_size
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, colour = title_colour)
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, plot.subtitle = element_text(size = subtitle_size
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, hjust = 0.5
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, colour = subtitle_colour)) +
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labs(title = bp_plot_title
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, x = xaxis_title
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, y = yaxis_title)
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, subtitle = subtitle_text
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, x = xaxis_title
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, y = yaxis_title)
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return(OutPlot_pos_count)
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}
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@ -22,7 +22,14 @@ stability_count_bp <- function(plotdf
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, leg_text_size = 20
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, leg_title_size = 22
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, yaxis_title = "Number of nsSNPs"
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, bp_plot_title = ""){
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, bp_plot_title = ""
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, label_categories = c("Destabilising", "Stabilising")
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, title_colour = "chocolate4"
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, subtitle_text = NULL
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, subtitle_size = 20
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, subtitle_colour = "pink"
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#, leg_position = c(0.73,0.8) # within plot area
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, leg_position = "top"){
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OutPlot_count = ggplot(plotdf, aes(x = eval(parse(text = df_colname)))) +
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geom_bar(aes(fill = eval(parse(text = df_colname))), show.legend = TRUE) +
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@ -35,14 +42,20 @@ stability_count_bp <- function(plotdf
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, axis.title.x = element_blank()
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, axis.title.y = element_text(size = axis_label_size)
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, axis.text.y = element_text(size = axis_text_size)
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, legend.position = c(0.73,0.8)
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, legend.position = leg_position
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, legend.text = element_text(size = leg_text_size)
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, legend.title = element_text(size = leg_title_size)
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, plot.title = element_text(size = axis_label_size)) +
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labs(title = bp_plot_title
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, y = yaxis_title) +
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, plot.title = element_text(size = axis_label_size
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, colour = title_colour)
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, plot.subtitle = element_text(size = subtitle_size
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, hjust = 0.5
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, colour = subtitle_colour)) +
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labs(title = bp_plot_title
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, subtitle = subtitle_text
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, y = yaxis_title) +
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scale_fill_discrete(name = leg_title
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, labels = c("Destabilising", "Stabilising"))
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#, labels = c("Destabilising", "Stabilising")
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, labels = label_categories)
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return(OutPlot_count)
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}
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@ -6,21 +6,24 @@ getwd()
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# load functions, data, dirs, hardocded vars
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# that will be used in testing the functions
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#===========================================
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source("plotting_data.R")
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infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
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drug = "streptomycin"
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gene = "gid"
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source("plotting_data.R")
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infile = paste0("~/git/Data/", drug, "/output/", gene, "_comb_stab_struc_params.csv")
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infile_df = read.csv(infile)
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lig_dist = 5
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pd_df = plotting_data(infile_df
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, lig_dist_colname = 'ligand_distance'
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, lig_dist_cutoff = lig_dist)
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pd_df = plotting_data(infile)
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my_df = pd_df[[1]]
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my_df_u = pd_df[[2]]
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my_df_u_lig = pd_df[[3]]
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dup_muts = pd_df[[4]]
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source("plotting_globals.R")
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drug = "streptomycin"
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gene = "gid"
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import_dirs(drug, gene)
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#=====================
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# functions to test
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#=====================
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@ -40,7 +43,9 @@ print(paste0("plot filename:", basic_bp_duet))
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# function only
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stability_count_bp(plotdf = my_df_u
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, df_colname = "duet_outcome"
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, leg_title = "DUET outcome")
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, leg_title = "DUET outcome"
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, label_categories = c("Destabilising", "Stabilising")
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, leg_position = "top")
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dev.off()
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@ -54,10 +59,13 @@ svg(plot_basic_bp_ligand)
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print(paste0("plot filename:", basic_bp_ligand))
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# function only
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lig_dist = 10
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stability_count_bp(plotdf = my_df_u_lig
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, df_colname = "ligand_outcome"
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, leg_title = "Ligand outcome"
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, bp_plot_title = "Sites < 10 Ang of ligand")
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, yaxis_title = paste0("Number of nsSNPs\nLigand dist: <", lig_dist, "\u212b")
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#, bp_plot_title = "Sites < 10 Ang of ligand"
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)
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dev.off()
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# ------------------------------
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