diff --git a/scripts/functions/bp_lineage.R b/scripts/functions/bp_lineage.R index ad43386..d21a465 100644 --- a/scripts/functions/bp_lineage.R +++ b/scripts/functions/bp_lineage.R @@ -4,11 +4,11 @@ # Lineage Diversity barplot ######################################## -lin_count_bp <- function( lf_data - , x_categ = "" - , y_count = "" - , bar_fill_categ = "" - , display_label_col = "" +lin_count_bp <- function( lf_data = lin_lf + , x_categ = "sel_lineages" + , y_count = "p_count" + , bar_fill_categ = "count_categ" + , display_label_col = "p_count" , bar_stat_stype = "identity" , x_lab_angle = 90 , d_lab_size = 5 @@ -20,13 +20,14 @@ lin_count_bp <- function( lf_data , my_xals = 22 # x axis label size , my_yals = 22 # y axis label size , my_lls = 22 # legend label size - , bar_col_labels = "" - , bar_col_values = "" + , bar_col_labels = c("Mutations", "Total Samples") + , bar_col_values = c("grey50", "gray75") , bar_leg_name = "" , leg_location = "top" , y_log10 = FALSE , y_scale_percent = FALSE , y_label = c("Count", "SNP diversity") + #, y_label = c("Count") ) { g = ggplot(lf_data , aes( x = factor( eval(parse(text = x_categ)), ordered = T ) diff --git a/scripts/functions/bp_subcolours.R b/scripts/functions/bp_subcolours.R index 91a8914..18089c9 100755 --- a/scripts/functions/bp_subcolours.R +++ b/scripts/functions/bp_subcolours.R @@ -36,9 +36,9 @@ ColourPalleteMulti = function(df, group, subgroup){ bp_stability_hmap <- function(plotdf = merged_df3 , xvar_colname = "position" #, bar_col_colname = "group" - , stability_colname = "" - , stability_outcome_colname = "" - , p_title = "" # "Protein stability (DUET)" + , stability_colname = "duet_scaled" + , stability_outcome_colname = "duet_outcome" + , p_title = "DUET" # "Protein stability (DUET)" , my_xaxls = 12 # x-axis label size , my_yaxls = 20 # y-axis label size , my_xaxts = 18 # x-axis text size diff --git a/scripts/functions/consurfP.R b/scripts/functions/consurfP.R index b80a095..22bb054 100644 --- a/scripts/functions/consurfP.R +++ b/scripts/functions/consurfP.R @@ -12,7 +12,7 @@ # wideP(): # input args #========================================================== -wideP_point <- function(plotdf +wideP_consurf <- function(plotdf , xvar_colname = "position" , yvar_colname = "consurf_score" , yvar_colourN_colname = "consurf_colour_rev" # num from 0-1 @@ -542,24 +542,51 @@ wideP_point <- function(plotdf }else{ cat("\nNo annotation for xvar requested") } + #============================================== if (A_xvar_lig){ - legs = grid.arrange(legend1 + legs = cowplot::plot_grid(legend1 , legend2 , ncol = 1 - , heights = c(3/4,1)) - out2 = grid.arrange( out + theme(legend.position = "none") - , legs - , ncol = 2 - , widths = c(9/10, 0.5/10) + , align = "hv" + , rel_heights = c(3/4,1)) + + out2 = cowplot::plot_grid( out + theme(legend.position = "none") + , legs + , ncol = 2 + , align = "hv" + , rel_widths = c(9/10, 0.5/10) ) }else{ - out2 = grid.arrange( out + theme(legend.position = "none") + out2 = cowplot::plot_grid( out + theme(legend.position = "none") , legend1 , ncol = 2 - , widths = c(9/10, 0.5/10) + , align = "hv" + , rel_widths = c(9/10, 0.5/10) ) } - + #============================================== + + + #============================================== + # if (A_xvar_lig){ + # legs = grid.arrange(legend1 + # , legend2 + # , ncol = 1 + # , heights = c(3/4,1)) + # + # out2 = grid.arrange( out + theme(legend.position = "none") + # , legs + # , ncol = 2 + # , widths = c(9/10, 0.5/10) + # ) + # }else{ + # out2 = grid.arrange( out + theme(legend.position = "none") + # , legend1 + # , ncol = 2 + # , widths = c(9/10, 0.5/10) + # ) + # } + #============================================== return(out2) #return(out2) diff --git a/scripts/functions/lf_bp.R b/scripts/functions/lf_bp.R index 675658e..90d7381 100644 --- a/scripts/functions/lf_bp.R +++ b/scripts/functions/lf_bp.R @@ -6,10 +6,10 @@ # beeswarm ############################# -lf_bp <- function(lf_df - , p_title = "" - , colour_categ = "" - , x_grp = "mutation_info" +lf_bp <- function(lf_df = lf_duet + , p_title = "DUET-DDG" + , colour_categ = "duet_outcome" + , x_grp = "mutation_info_labels" , y_var = "param_value" , facet_var = "param_type" , n_facet_row = 1 diff --git a/scripts/functions/stability_count_bp.R b/scripts/functions/stability_count_bp.R index e5ed684..f6cd975 100644 --- a/scripts/functions/stability_count_bp.R +++ b/scripts/functions/stability_count_bp.R @@ -15,8 +15,8 @@ theme_set(theme_grey()) ## ...opt args #========================================================== stability_count_bp <- function(plotdf - , df_colname = "" - , leg_title = "Legend Title" + , df_colname = "duet_outcome" + , leg_title = "DUET" , ats = 25 # axis text size , als = 22 # axis label size , lts = 20 # legend text size diff --git a/scripts/functions/tests/test_bp.R b/scripts/functions/tests/test_bp.R index bdb48ca..020a947 100644 --- a/scripts/functions/tests/test_bp.R +++ b/scripts/functions/tests/test_bp.R @@ -5,19 +5,18 @@ getwd() #=========================================== # load functions, data, dirs, hardocded vars # that will be used in testing the functions +#drug = "streptomycin" +#gene = "gid" +#source("plotting_data.R") +#infile = paste0("~/git/Data/", drug, "/output/", gene, "_comb_stab_struc_params.csv") +#infile_df = read.csv(infile) + + #=========================================== -drug = "streptomycin" -gene = "gid" - -source("plotting_data.R") - -infile = paste0("~/git/Data/", drug, "/output/", gene, "_comb_stab_struc_params.csv") -infile_df = read.csv(infile) - lig_dist = 5 pd_df = plotting_data(infile_df , lig_dist_colname = 'ligand_distance' - , lig_dist_cutoff = lig_dist) + , lig_dist_cutoff = lig_dist) my_df = pd_df[[1]] my_df_u = pd_df[[2]] @@ -42,8 +41,8 @@ print(paste0("plot filename:", basic_bp_duet)) # function only stability_count_bp(plotdf = my_df_u - , df_colname = "duet_outcome" - , leg_title = "DUET outcome" + , df_colname = "ligand_outcome" + , leg_title = "Lig outcome" , label_categories = c("Destabilising", "Stabilising") , leg_position = "top") diff --git a/scripts/functions/tests/test_bp_lineage.R b/scripts/functions/tests/test_bp_lineage.R index 876f237..a198b82 100644 --- a/scripts/functions/tests/test_bp_lineage.R +++ b/scripts/functions/tests/test_bp_lineage.R @@ -20,8 +20,8 @@ levels(lin_lf_plot$sel_lineages_f) #========================= # Lineage count plot #========================= -lin_count_bp(lin_lf_plot - , x_categ = "sel_lineages_f" +lin_count_bp(lin_lf_plot = lin_lf + , x_categ = "sel_lineages" , y_count = "p_count" , bar_fill_categ = "count_categ" , display_label_col = "p_count" @@ -51,8 +51,8 @@ levels(lin_wf_plot$sel_lineages_f) #========================= # Lineage Diversity plot #========================= -lin_count_bp(lin_wf_plot - , x_categ = "sel_lineages_f" +lin_count_bp(lin_wf_plot = lin_wf + , x_categ = "sel_lineages" , y_count = "snp_diversity" , display_label_col = "snp_diversity_f" , bar_stat_stype = "identity" diff --git a/scripts/functions/tests/test_consurfP.R b/scripts/functions/tests/test_consurfP.R index ed32a50..8ac8750 100644 --- a/scripts/functions/tests/test_consurfP.R +++ b/scripts/functions/tests/test_consurfP.R @@ -4,9 +4,9 @@ library(ggplot2) library(tidyverse) library(cowplot) library(gridExtra) -source("consurf_plot_func.R") +source("~/git/LSHTM_analysis/scripts/functions/consurfP.R") -# ########################################################################### +############################################################################ # merged_df3 = read.csv("~/git/Data/cycloserine/output/alr_all_params.csv"); source("~/git/LSHTM_analysis/config/alr.R") # if ( tolower(gene) == "alr") { # aa_pos_lig1 = NULL @@ -15,13 +15,13 @@ source("consurf_plot_func.R") # p_title = gene # } ########################################################################### -# merged_df3 = read.csv("~/git/Data/ethambutol/output/embb_all_params.csv"); source("~/git/LSHTM_analysis/config/embb.R") -# if ( tolower(gene) == "embb") { -# aa_pos_lig1 = aa_pos_ca -# aa_pos_lig2 = aa_pos_cdl -# aa_pos_lig3 = aa_pos_dsl -# p_title = gene -# } +merged_df3 = read.csv("~/git/Data/ethambutol/output/embb_all_params.csv"); source("~/git/LSHTM_analysis/config/embb.R") +if ( tolower(gene) == "embb") { + aa_pos_lig1 = aa_pos_ca + aa_pos_lig2 = aa_pos_cdl + aa_pos_lig3 = aa_pos_dsl + p_title = gene +} ########################################################################### # merged_df3 = read.csv("~/git/Data/streptomycin/output/gid_all_params.csv"); source("~/git/LSHTM_analysis/config/gid.R") # if ( tolower(gene) == "gid") { @@ -47,13 +47,13 @@ source("consurf_plot_func.R") # p_title = gene # } ########################################################################### -merged_df3 = read.csv("~/git/Data/rifampicin/output/rpob_all_params.csv"); source("~/git/LSHTM_analysis/config/rpob.R") -if ( tolower(gene) == "rpob") { - aa_pos_lig1 = NULL - aa_pos_lig2 = NULL - aa_pos_lig3 = NULL - p_title = gene -} +# merged_df3 = read.csv("~/git/Data/rifampicin/output/rpob_all_params.csv"); source("~/git/LSHTM_analysis/config/rpob.R") +# if ( tolower(gene) == "rpob") { +# aa_pos_lig1 = NULL +# aa_pos_lig2 = NULL +# aa_pos_lig3 = NULL +# p_title = gene +# } ######################################################################### consurf_palette1 = c("0" = "yellow2" @@ -84,21 +84,21 @@ consurf_palette2 = c("0" = "yellow2" aa_pos_hbond = c(2, 4) aa_pos_other = c(3, 4, 14, 10) -wideP_point (plotdf = merged_df3 +wideP_consurf(plotdf = merged_df3 , xvar_colname = "position" , yvar_colname = "consurf_score" , yvar_colourN_colname = "consurf_colour_rev" , ylab = "Consurf score" - , plot_error_bars = F + , plot_error_bars = T , upper_EB_colname = "consurf_ci_upper" , lower_EB_colname = "consurf_ci_lower" , plot_type = "point" , point_colours = consurf_palette2 , leg_title1 = "Consurf" , leg_labels = c("0"="Insufficient Data" - , "1"= "Variable" + , "1" = "Variable" , "2", "3", "4", "5", "6", "7", "8" - , "9"= "Conserved") + , "9" = "Conserved") # axes title and label sizes , x_axts = 8 diff --git a/scripts/functions/tests/test_corr_plot_data.R b/scripts/functions/tests/test_corr_plot_data.R index 4376a58..24243e9 100644 --- a/scripts/functions/tests/test_corr_plot_data.R +++ b/scripts/functions/tests/test_corr_plot_data.R @@ -4,4 +4,5 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") m3 = corr_data_extract(merged_df3); head(m3) m2 = corr_data_extract(meregd_df2); head(m2) -m3S = corr_data_extract(merged_df3, extract_scaled_cols = T); head(m3S) \ No newline at end of file +m3S = corr_data_extract(merged_df3, extract_scaled_cols = T); head(m3S) + diff --git a/scripts/functions/tests/test_lf_bp.R b/scripts/functions/tests/test_lf_bp.R index 2102585..e026c3c 100644 --- a/scripts/functions/tests/test_lf_bp.R +++ b/scripts/functions/tests/test_lf_bp.R @@ -15,7 +15,7 @@ source("../functions/lf_bp.R") lf_bp(lf_df = lf_encomddg , p_title = "ENCoM-DDG" , colour_categ = "ddg_encom_outcome" - , x_grp = "mutation_info" + , x_grp = "mutation_info_labels" , y_var = "param_value" , facet_var = "param_type" , n_facet_row = 1 diff --git a/scripts/functions/tests/test_logo_plots.R b/scripts/functions/tests/test_logo_plots.R index cf38699..1414876 100644 --- a/scripts/functions/tests/test_logo_plots.R +++ b/scripts/functions/tests/test_logo_plots.R @@ -1,5 +1,5 @@ -source("~/git/LSHTM_analysis/config/gid.R") -#source("~/git/LSHTM_analysis/config/pnca.R") +#source("~/git/LSHTM_analysis/config/gid.R") +source("~/git/LSHTM_analysis/config/pnca.R") #source("~/git/LSHTM_analysis/config/embb.R") #source("~/git/LSHTM_analysis/config/katg.R") #source("~/git/LSHTM_analysis/config/alr.R") @@ -12,7 +12,7 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") # mainly OR # script: logoP_or.R ################################ -LogoPlotCustomH (plot_df = merged_df3 +LP1<- LogoPlotCustomH (plot_df = merged_df3 , x_axis_colname = "position" , y_axis_colname = "or_mychisq" , symbol_colname = "mutant_type" @@ -25,10 +25,10 @@ LogoPlotCustomH (plot_df = merged_df3 , y_lab = "Odds Ratio" , x_ats = 10 # text size , x_tangle = 90 # text angle - , y_ats = 22 + , y_ats = 15 , y_tangle = 0 - , x_tts = 19 # title size - , y_tts = 22 + , x_tts = 13 # title size + , y_tts = 13 #, leg_pos = c(0.05,-0.12) , leg_pos = "top" , leg_dir = "horizontal" @@ -36,30 +36,29 @@ LogoPlotCustomH (plot_df = merged_df3 , leg_tts = 16 # leg title size ) - ######################################## # Logo plot showing nsSNPs by positions # wild-type and mutant aa # script: logoP_snp.R ######################################## -LogoPlotSnps(plot_df = merged_df3 +LP2<- LogoPlotSnps(plot_df = merged_df3 , x_axis_colname = "position" , symbol_mut_colname = "mutant_type" , symbol_wt_colname = "wild_type" - , omit_snp_count = c(1)# can be 0,1, 2, etc. - , my_logo_col = "chemistry" + , omit_snp_count = c(1)# can be 0,1, 2, etc.# DD + , my_logo_col = "chemistry" #DD , x_lab = "Wild-type position" , y_lab = "nsSNP count" - , x_ats = 10 # text size - , x_tangle = 90 # text angle - , y_ats = 18 + , x_ats = 10 + , x_tangle = 90 + , y_ats = 15 , y_tangle = 0 - , x_tts = 18 # title size - , y_tts = 18 + , x_tts = 13 + , y_tts = 13 , leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9) , leg_dir = "horizontal" # can be vertical or horizontal - , leg_ts = 14 # leg text size - , leg_tts = 16 # leg title size + , leg_ts = 14 + , leg_tts = 16 ) #################################################### @@ -76,13 +75,12 @@ LogoPlotSnps(plot_df = merged_df3 # to select a small dataset: see test_ed_pfm_data.R ##################################################### - -LogoPlotMSA(msaSeq_mut = msa_seq +LP3<- LogoPlotMSA(msaSeq_mut = msa_seq , msaSeq_wt = wt_seq , logo_type = c("EDLogo") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw") , EDScore_type = c("log") , bg_prob = NULL - , my_logo_col = "taylor" + , my_logo_col = "chemistry" #, plot_positions = c(5:10, 92, 195, 118:119) , x_axis_offset = 0.02 , x_axis_offset_filtered = 0.05 @@ -101,3 +99,14 @@ LogoPlotMSA(msaSeq_mut = msa_seq , leg_ts = 16 , leg_tts = 16 ) + + + +out_logoP = cowplot::plot_grid(LP3, LP1, LP2 + , nrow = 3 + , ncol = 1 + , rel_width = c(1/3, 0.5/3, 1/3) + , rel_heights = c(1, 1, 1) + , align = "hv") + +out_logoP