83 lines
2.9 KiB
R
83 lines
2.9 KiB
R
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)
|