modified bp with option for adding stats and boxplplots. Moved old one to redundant

2021-09-02 12:50:24 +01:00 · 2021-09-02 12:50:24 +01:00 · fcb4b85747
commit fcb4b85747
parent 826d3c72b7
8 changed files with 443 additions and 102 deletions
--- a/scripts/functions/redundant/test_lf_bp_with_stats.R
+++ b/scripts/functions/redundant/test_lf_bp_with_stats.R
@ -0,0 +1,83 @@
+setwd("~/git/LSHTM_analysis/scripts/plotting/")
+
+source("../functions/lf_bp_with_stats.R")
+source("../functions/lf_bp.R")
+
+######################
+# Make  plot
+######################
+# Note: Data
+# run other_plots_data.R
+# to get the long format data to test this function 
+
+lf_bp(lf_df = lf_dynamut2
+                       , p_title = "Dynamut2"
+                       , colour_categ = "ddg_dynamut2_outcome"
+                       , x_grp = "mutation_info"
+                       , y_var = "param_value"
+                       , facet_var = "param_type"
+                       , n_facet_row = 1
+                       , y_scales = "free_y"
+                       , colour_bp_strip = "khaki2"
+                       , dot_size = 3
+                       , dot_transparency = 0.3
+                       , violin_quantiles = c(0.25, 0.5, 0.75)
+                       , my_ats = 22 # axis text size
+                       , my_als = 20 # axis label size
+                       , my_fls = 20 # facet label size
+                       , my_pts = 22 # plot title size 
+                       , make_boxplot = F
+                       , bp_width = "auto"
+                       , add_stats = T
+                       , stat_grp_comp = c("DM", "OM")
+                       , stat_method = "wilcox.test"
+                       , my_paired = FALSE
+                       , stat_label = c("p.format", "p.signif") )
+ 
+# foo = lf_dynamut2 %>%
+#   group_by(mutation_info, param_type) %>%
+#   summarise( Mean = mean(param_value, na.rm = T)
+#              , SD = sd(param_value, na.rm = T)
+#              , Median = median(param_value, na.rm = T)
+#              , IQR = IQR(param_value, na.rm = T) )
+
+# Quick tests
+plotdata_sel = subset(lf_dynamut2
+             , lf_dynamut2$param_type == "ASA")
+
+plot_sum = plotdata_sel %>%
+  group_by(mutation_info, param_type) %>%
+  summarise(n = n()
+             , Mean = mean(param_value, na.rm = T)
+             , SD = sd(param_value, na.rm = T)
+             , Min = min(param_value, na.rm = T)
+             , Q1 = quantile(param_value, na.rm = T, 0.25)
+             , Median = median(param_value, na.rm = T)
+             , Q3 = quantile(param_value, na.rm = T, 0.75)
+             , Max = max(param_value, na.rm = T) ) %>%
+  rename('Mutation Class' = mutation_info
+         , Parameter = param_type)
+plot_sum = as.data.frame(plot_sum, row.names = NULL)
+plot_sum
+
+bar = compare_means(param_value ~ mutation_info
+              , group.by = "param_type"
+              , data = plotdata_sel
+              , paired = FALSE
+              , p.adjust.method = "BH")
+bar2 = bar[c("param_type"
+              , "group1"
+              , "group2"
+              , "p.format"
+              , "p.signif"
+              , "p.adj")] %>%
+  rename(Parameter = param_type
+          , Group1 = group1
+          , Group2 = group2
+          , "P-value" = p.format
+          , "P-sig" = p.signif
+          , "P-adj" = p.adj)
+bar2 = data.frame(bar2); bar2
+
+library(Hmisc)
+describe(lf_dynamut2)