diff --git a/scripts/functions/lf_unpaired_stats.R b/scripts/functions/lf_unpaired_stats.R new file mode 100644 index 0000000..28a8ad0 --- /dev/null +++ b/scripts/functions/lf_unpaired_stats.R @@ -0,0 +1,21 @@ +library(ggpubr) +################################################################### + +lf_unpaired_stats <- function(lf_data + , lf_stat_value = "param_value" + , lf_stat_group = "mutation_info" + , lf_col_statvars = "param_type" + , my_paired = FALSE + , stat_adj = "none"){ + + stat_formula = as.formula(paste0(lf_stat_value, "~", lf_stat_group)) + + my_stat_df = compare_means(stat_formula + , group.by = lf_col_statvars + , data = lf_data + , paired = my_paired + , p.adjust.method = stat_adj) + + + return(my_stat_df) +} \ No newline at end of file diff --git a/scripts/functions/stat_bp_stability.R b/scripts/functions/stat_bp_stability.R index a34b66f..8ca4a7f 100644 --- a/scripts/functions/stat_bp_stability.R +++ b/scripts/functions/stat_bp_stability.R @@ -1,8 +1,49 @@ -my_stat_ps = compare_means(param_value~mutation_info, group.by = "param_type" - , data = df_lf_ps, paired = FALSE, p.adjust.method = "BH") +library(ggpubr) +################################################################### + +my_unpaired_stats <- function(lf_data + , lf_stat_value = "param_value" + , lf_stat_group = "mutation_info" + , lf_col_statvars = "param_type" + , my_paired = FALSE + , stat_adj = "none"){ + + stat_formula = as.formula(paste0(lf_stat_value, "~", lf_stat_group)) + + my_stat_df = compare_means(stat_formula + , group.by = lf_col_statvars + , data = lf_data + , paired = my_paired + , p.adjust.method = stat_adj) + + + return(my_stat_df) +} + +##################### +# call stat function +##################### +stat_results_df <- my_unpaired_stats(lf_data = lf_duet + , lf_stat_value = "param_value" + , lf_stat_group = "mutation_info" + , lf_col_statvars = "param_type" + , my_paired = FALSE + , stat_adj = "none" +) y_value = "param_value" +################################# +my_comparisons <- list( c("DM", "OM") ) + +my_ats = 22 # axis text size +my_als = 20 # axis label size +my_fls = 20 # facet label size +my_pts = 22 # plot title size + +#################################### + + stat_bp_mut <- function(df , x_bp_cateog = "mutation_info" , y_var = "param_value" @@ -16,7 +57,12 @@ stat_bp_mut <- function(df #, stat_label = "p.format") , stat_label = "p.signif" ) -p1 = ggplot(df_lf_ps, aes(x = mutation_info + +############################# +y_value = "param_value" + + +p1 = ggplot(lf_duet, aes(x = mutation_info , y = eval(parse(text = y_value)) )) + facet_wrap(~ param_type , nrow = 1 @@ -48,4 +94,7 @@ p1 = ggplot(df_lf_ps, aes(x = mutation_info , method = "wilcox.test" , paired = FALSE #, label = "p.format") - , label = "p.signif") \ No newline at end of file + , label = "p.signif") + +p1 + diff --git a/scripts/functions/test_lf_unpaired_stats.R b/scripts/functions/test_lf_unpaired_stats.R new file mode 100644 index 0000000..9ec4aac --- /dev/null +++ b/scripts/functions/test_lf_unpaired_stats.R @@ -0,0 +1,17 @@ +setwd("~/git/LSHTM_analysis/scripts/functions") +source("lf_unpaired_stats.R") + +# run other_plots_data.R +# to get the df you want to test this function + + +##################### +# call stat function +##################### +stat_results_df <- lf_unpaired_stats(lf_data = lf_duet + , lf_stat_value = "param_value" + , lf_stat_group = "mutation_info" + , lf_col_statvars = "param_type" + , my_paired = FALSE + , stat_adj = "none" +) \ No newline at end of file diff --git a/scripts/plotting/other_plots_data.R b/scripts/plotting/other_plots_data.R index 8fc9e00..d2229b8 100644 --- a/scripts/plotting/other_plots_data.R +++ b/scripts/plotting/other_plots_data.R @@ -6,7 +6,7 @@ #======================================================================= # working dir and loading libraries # getwd() -# setwd("~/git/LSHTM_analysis/scripts/plotting") +setwd("~/git/LSHTM_analysis/scripts/plotting") # getwd() # make cmd @@ -14,7 +14,7 @@ # drug = "streptomycin" # gene = "gid" -#source("get_plotting_dfs.R") +source("get_plotting_dfs.R") #======================================================================= # MOVE TO COMBINE or singular file for deepddg @@ -492,47 +492,47 @@ if (nrow(lf_mcsm) == expected_rows_lf){ quit() } ############################################################################ -# # clear excess variables -# rm(all_plot_dfs -# , cols_dynamut2_df -# , cols_mcsm_df -# , cols_mcsm_na_df -# , comb_df -# , corr_data_ps -# , corr_ps_df3 -# , df_lf_ps -# , foo -# , foo_cnames -# , gene_metadata -# , logo_data -# , logo_data_or_mult -# , logo_data_plot -# , logo_data_plot_logor -# , logo_data_plot_or -# , my_data_snp -# , my_df -# , my_df_u -# , ols_mcsm_df -# , other_muts -# , pd_df -# , subcols_df_ps -# , tab_mt -# , wide_df_logor -# , wide_df_logor_m -# , wide_df_or -# , wide_df_or_mult -# , wt) -# -# -# rm(c3, c4, check1 -# , cols_check -# , cols_to_select -# , cols_to_select_deepddg -# , cols_to_select_duet -# , cols_to_select_dynamut -# , cols_to_select_dynamut2 -# , cols_to_select_encomddg -# , cols_to_select_encomdds -# , cols_to_select_mcsm -# , cols_to_select_mcsm_na -# , cols_to_select_sdm) +# clear excess variables +rm(all_plot_dfs + , cols_dynamut2_df + , cols_mcsm_df + , cols_mcsm_na_df + , comb_df + , corr_data_ps + , corr_ps_df3 + , df_lf_ps + , foo + , foo_cnames + , gene_metadata + , logo_data + , logo_data_or_mult + , logo_data_plot + , logo_data_plot_logor + , logo_data_plot_or + , my_data_snp + , my_df + , my_df_u + , ols_mcsm_df + , other_muts + , pd_df + , subcols_df_ps + , tab_mt + , wide_df_logor + , wide_df_logor_m + , wide_df_or + , wide_df_or_mult + , wt) + + +rm(c3, c4, check1 + , cols_check + , cols_to_select + , cols_to_select_deepddg + , cols_to_select_duet + , cols_to_select_dynamut + , cols_to_select_dynamut2 + , cols_to_select_encomddg + , cols_to_select_encomdds + , cols_to_select_mcsm + , cols_to_select_mcsm_na + , cols_to_select_sdm)