breakage
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5 changed files with 74 additions and 12 deletions
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@ -23,14 +23,19 @@ lin_count_bp_diversity <- function( lf_data = lin_wf
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, my_xals = 22 # x axis label size
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, my_yals = 22 # y axis label size
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, my_lls = 22 # legend label size
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, bar_col_labels = c("Mutations", "Total Samples")
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, bar_col_values = c("grey50", "gray75")
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, bar_col_labels = "" #c("Mutations", "Total Samples")
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, bar_col_values = c("gray50", "gray75")
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, bar_leg_name = ""
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, leg_location = "top"
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, y_log10 = FALSE
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, y_scale_percent = FALSE
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#, y_label = c("Count", "SNP diversity")
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, y_label = c("SNP diversity")
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, bp_plot_title = ""
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, title_colour = "chocolate4"
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, subtitle_text = NULL
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, sts = 20
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, subtitle_colour = "#350E20FF" #brown
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) {
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if(!all_lineages){
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lf_data = lf_data[lf_data[[x_categ]]%in%use_lineages,]
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@ -58,7 +63,13 @@ lin_count_bp_diversity <- function( lf_data = lin_wf
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, axis.title.y = element_text(size = my_yals
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, colour = "black")
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, legend.position = leg_location
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, legend.text = element_text(size = my_lls)) +
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, legend.text = element_text(size = my_lls)
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, plot.title = element_text(size = my_lls
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, colour = title_colour
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, hjust = 0.5)
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, plot.subtitle = element_text(size = sts
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, hjust = 0.5
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, colour = subtitle_colour)) +
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geom_label(aes(label = eval(parse(text = display_label_col)))
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, size = d_lab_size
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@ -72,10 +83,16 @@ lin_count_bp_diversity <- function( lf_data = lin_wf
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scale_fill_manual(values = bar_col_values
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, name = bar_leg_name
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, labels = bar_col_labels) +
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labs(title = ""
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, x = ""
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, y = y_label
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, colour = "black")
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# labs(title = ""
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# , x = ""
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# , y = y_label
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# , colour = "black")
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#
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labs(title = bp_plot_title
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, subtitle = subtitle_text
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, x = ""
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, y = y_label
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, colour = "black")
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if (y_log10){
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@ -90,10 +107,11 @@ lin_count_bp_diversity <- function( lf_data = lin_wf
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scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
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#scale_y_continuous(labels = scales::percent) +
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labs(title = ""
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, x = ""
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, y = y_label
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, colour = "black")
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labs(title = bp_plot_title
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, subtitle = subtitle_text
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, x = ""
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, y = y_label
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, colour = "black")
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}
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return(OutPlot)
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@ -343,6 +343,29 @@ combining_dfs_plotting <- function( my_df_u
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, "\nNo. of rows merged_df3: ", nrow(merged_df3))
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quit()
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}
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#---------------------------------------------
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# add columns that are needed to generate plots with revised colnames and strings
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#----------------------------------------------
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merged_df3['sensitivity'] = ifelse(merged_df3['dst_mode'] == 1, "R", "S")
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merged_df3['mutation_info_labels'] = ifelse(merged_df3['mutation_info_labels'] == "DM", "R", "S")
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merged_df2['sensitivity'] = ifelse(merged_df2['dst_mode'] == 1, "R", "S")
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merged_df2['mutation_info_labels'] = ifelse(merged_df2['mutation_info_labels'] == "DM", "R", "S")
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#check1 = all(table(merged_df3["mutation_info_labels"]) == table(merged_df3['sensitivity']))
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#check2 = all(table(merged_df2["mutation_info_labels"]) == table(merged_df2['sensitivity']))
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check1 = all(merged_df3["mutation_info_labels"] == merged_df3['sensitivity'])
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check2 = all(merged_df2["mutation_info_labels"] == merged_df2['sensitivity'])
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if(check1 && check2){
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cat("PASS: merged_df3 and merged_df2 have mutation info labels as R and S"
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, "\nIt also has sensitivity column"
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, "\nThese are identical")
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}else{
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stop("Abort: merged_df3 or merged_df2 can't be created because of lable mismatch")
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}
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return(list( merged_df2
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, merged_df3
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))
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@ -37,6 +37,11 @@
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#1) df to choose (merged_df3 or merged_df2)
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#2)
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##################################################################
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DistCutOff = 10
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LigDist_colname # = "ligand_distance" # from globals
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ppi2Dist_colname = "interface_dist"
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naDist_colname = "TBC"
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dm_om_wf_lf_data <- function(df
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, gene_name = gene # from globals
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, colnames_to_extract
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@ -51,6 +56,15 @@ dm_om_wf_lf_data <- function(df
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, dr_other_muts_labels = c("DM", "OM") # only used if ^^ = ""
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, categ_cols_to_factor){
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df = as.data.frame(df)
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df['sensitivity'] = ifelse(df['dst_mode'] == 1, "R", "S")
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table(df['sensitivity'])
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df[[mut_info_label_colname]] = ifelse(df[[mut_info_label_colname]] == "DM", "R", "S")
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table(df[[mut_info_label_colname]])
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# Initialise the required dfs based on gene name
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geneL_normal = c("pnca")
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#geneL_na_dy = c("gid")
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@ -124,6 +138,7 @@ dm_om_wf_lf_data <- function(df
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, mut_colname, mut_info_colname, mut_info_label_colname
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, aa_pos_colname
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, LigDist_colname
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, ppi2Dist_colname, naDist_colname
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, "duet_stability_change" , "duet_scaled" , "duet_outcome"
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, "ligand_affinity_change", "affinity_scaled" , "ligand_outcome"
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, "ddg_foldx" , "foldx_scaled" , "foldx_outcome"
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