modified bp with option for adding stats and boxplplots. Moved old one to redundant
This commit is contained in:
parent
826d3c72b7
commit
fcb4b85747
8 changed files with 443 additions and 102 deletions
193
scripts/functions/lf_bp.R
Normal file
193
scripts/functions/lf_bp.R
Normal file
|
|
@ -0,0 +1,193 @@
|
|||
#############################
|
||||
# Barplots: ggplot
|
||||
# stats +/-
|
||||
# violin +/-
|
||||
# barplot +/
|
||||
# beeswarm
|
||||
#############################
|
||||
|
||||
lf_bp <- function(lf_df
|
||||
, p_title = ""
|
||||
, colour_categ = ""
|
||||
, 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) # can be NULL
|
||||
, 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 = FALSE
|
||||
, bp_width = c("auto", 0.5)
|
||||
, add_stats = FALSE
|
||||
, stat_grp_comp = c("DM", "OM")
|
||||
, stat_method = "wilcox.test"
|
||||
, my_paired = FALSE
|
||||
, stat_label = c("p.format", "p.signif") ){
|
||||
|
||||
p1 <- ggplot(lf_df, aes(x = eval(parse(text = x_grp))
|
||||
, y = eval(parse(text = y_var)) )) +
|
||||
|
||||
facet_wrap(~ eval(parse(text = facet_var))
|
||||
, nrow = n_facet_row
|
||||
, scales = y_scales) +
|
||||
|
||||
geom_violin(trim = T
|
||||
, scale = "width"
|
||||
#, position = position_dodge(width = 0.9)
|
||||
, draw_quantiles = violin_quantiles)
|
||||
|
||||
if (make_boxplot){
|
||||
|
||||
if (bp_width == "auto"){
|
||||
bp_width = 0.5/length(unique(lf_df[[x_grp]]))
|
||||
cat("\nAutomatically calculated boxplot width, using bp_width:\n", bp_width, "\n")
|
||||
}else{
|
||||
cat("\nBoxplot width value provided, using:", bp_width, "\n")
|
||||
bp_width = bp_width}
|
||||
|
||||
p2 = p1 + geom_boxplot(fill = "white"
|
||||
, outlier.colour = NA
|
||||
#, position = position_dodge(width = 0.9)
|
||||
, width = bp_width) +
|
||||
geom_beeswarm(priority = "density"
|
||||
#, shape = 21
|
||||
, size = dot_size
|
||||
, alpha = dot_transparency
|
||||
, show.legend = FALSE
|
||||
, cex = 0.8
|
||||
, aes(colour = factor(eval(parse(text = colour_categ))) ))
|
||||
|
||||
} else {
|
||||
# ggbeeswarm (better than geom_point)
|
||||
p2 = p1 + geom_beeswarm(priority = "density"
|
||||
#, shape = 21
|
||||
, size = dot_size
|
||||
, alpha = dot_transparency
|
||||
, show.legend = FALSE
|
||||
, cex = 0.8
|
||||
, aes(colour = factor(eval(parse(text = colour_categ))) ))
|
||||
}
|
||||
|
||||
# Add foramtting to graph
|
||||
OutPlot = p2 + theme(axis.text.x = element_text(size = my_ats)
|
||||
, axis.text.y = element_text(size = my_ats
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_text(size = my_ats)
|
||||
, axis.title.y = element_text(size = my_ats)
|
||||
, plot.title = element_text(size = my_pts
|
||||
, hjust = 0.5
|
||||
, colour = "black"
|
||||
, face = "bold")
|
||||
, strip.background = element_rect(fill = colour_bp_strip)
|
||||
, strip.text.x = element_text(size = my_fls
|
||||
, colour = "black")
|
||||
, legend.title = element_text(color = "black"
|
||||
, size = my_als)
|
||||
, legend.text = element_text(size = my_ats)
|
||||
, legend.direction = "vertical") +
|
||||
|
||||
labs(title = p_title
|
||||
, x = ""
|
||||
, y = "")
|
||||
|
||||
if (add_stats){
|
||||
my_comparisonsL <- list( stat_grp_comp )
|
||||
|
||||
OutPlot = OutPlot + stat_compare_means(comparisons = my_comparisonsL
|
||||
, method = stat_method
|
||||
, paired = my_paired
|
||||
, label = stat_label[1])
|
||||
}
|
||||
return(OutPlot)
|
||||
}
|
||||
|
||||
#############################
|
||||
# Barplot NO stats: plotly
|
||||
# violin +/-
|
||||
# barplot +/
|
||||
# beeswarm
|
||||
|
||||
# TODO: plot_ly()
|
||||
#############################
|
||||
lf_bp_plotly <- function(lf_df
|
||||
, p_title = ""
|
||||
, colour_categ = ""
|
||||
, 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) # can be NULL
|
||||
, my_ats = 20 # axis text size
|
||||
, my_als = 18 # axis label size
|
||||
, my_fls = 18 # facet label size
|
||||
, my_pts = 22 # plot title size)
|
||||
#, make_boxplot = FALSE
|
||||
, bp_width = c("auto", 0.5)
|
||||
#, add_stats = FALSE
|
||||
#, stat_grp_comp = c("DM", "OM")
|
||||
#, stat_method = "wilcox.test"
|
||||
#, my_paired = FALSE
|
||||
#, stat_label = c("p.format", "p.signif")
|
||||
){
|
||||
|
||||
OutPlotly = ggplot(lf_df, aes(x = eval(parse(text = x_grp))
|
||||
, y = eval(parse(text = y_var))
|
||||
, label1 = x_grp
|
||||
, label2 = y_var
|
||||
, lable3 = colour_categ) ) +
|
||||
|
||||
facet_wrap(~ eval(parse(text = facet_var))
|
||||
, nrow = n_facet_row
|
||||
, scales = y_scales) +
|
||||
|
||||
geom_violin(trim = T
|
||||
, scale = "width"
|
||||
, draw_quantiles = violin_quantiles) +
|
||||
|
||||
geom_beeswarm(priority = "density"
|
||||
, size = dot_size
|
||||
, alpha = dot_transparency
|
||||
, show.legend = FALSE
|
||||
, cex = 0.8
|
||||
, aes(colour = factor(eval(parse(text = colour_categ) ) ) ) ) +
|
||||
theme(axis.text.x = element_text(size = my_ats)
|
||||
, axis.text.y = element_text(size = my_ats
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_text(size = my_ats)
|
||||
, axis.title.y = element_text(size = my_ats)
|
||||
, plot.title = element_text(size = my_pts
|
||||
, hjust = 0.5
|
||||
, colour = "black"
|
||||
, face = "bold")
|
||||
, strip.background = element_rect(fill = colour_bp_strip)
|
||||
, strip.text.x = element_text(size = my_fls
|
||||
, colour = "black")
|
||||
, legend.title = element_text(color = "black"
|
||||
, size = my_als)
|
||||
, legend.text = element_text(size = my_ats)
|
||||
, legend.position = "none")+
|
||||
|
||||
labs(title = p_title
|
||||
, x = ""
|
||||
, y = "")
|
||||
|
||||
OutPlotly = ggplotly(OutPlotly
|
||||
#, tooltip = c("label")
|
||||
)
|
||||
return(OutPlotly)
|
||||
|
||||
}
|
||||
|
|
@ -14,13 +14,23 @@ lf_bp_with_stats <- function(lf_df
|
|||
, stat_grp_comp = c("DM", "OM")
|
||||
, stat_method = "wilcox.test"
|
||||
, my_paired = FALSE
|
||||
#, stat_label = "p.format")
|
||||
, bp_width = c("auto", 0.5)
|
||||
, dot_size = 3
|
||||
, dot_transparency = 0.3
|
||||
, stat_label = c("p.format", "p.signif")
|
||||
, my_ats = 22 # axis text size
|
||||
, my_als = 20 # axis label size
|
||||
, my_fls = 20 # facet label size
|
||||
, my_pts = 22 # plot title size
|
||||
) {
|
||||
if (bp_width == "auto"){
|
||||
bp_width = 0.5/length(unique(lf_df[[x_grp]]))
|
||||
cat("\nAutomatically calculated boxplot width, using bp_width:\n", bp_width, "\n")
|
||||
}else{
|
||||
cat("\nBoxplot width value provided, using:", bp_width, "\n")
|
||||
bp_width = bp_width
|
||||
}
|
||||
|
||||
my_comparisonsL <- list( stat_grp_comp )
|
||||
|
||||
bp_statP <- ggplot(lf_df, aes(x = eval(parse(text = x_grp))
|
||||
|
|
@ -30,15 +40,30 @@ lf_bp_with_stats <- function(lf_df
|
|||
, nrow = n_facet_row
|
||||
, scales = y_scales) +
|
||||
|
||||
geom_boxplot(fill = "white", outlier.colour = NA
|
||||
#, position = position_dodge(width = 0.9)
|
||||
, width = 0.2) +
|
||||
|
||||
geom_point(position = position_jitterdodge(dodge.width = 0.01)
|
||||
, alpha = 0.5
|
||||
, show.legend = FALSE
|
||||
, aes(colour = factor(eval(parse(text = colour_categ))) )) +
|
||||
geom_violin(trim = T
|
||||
, scale = "width"
|
||||
#, position = position_dodge(width = 0.9)
|
||||
, draw_quantiles = c(0.25, 0.5, 0.75)) +
|
||||
|
||||
# geom_boxplot(fill = "white"
|
||||
# , outlier.colour = NA
|
||||
# #, position = position_dodge(width = 0.9)
|
||||
# , width = bp_width) +
|
||||
|
||||
# geom_point(position = position_jitterdodge(dodge.width = 0.5)
|
||||
# , alpha = 0.5
|
||||
# , show.legend = FALSE
|
||||
# , aes(colour = factor(eval(parse(text = colour_categ))) )) +
|
||||
|
||||
# ggbeeswarm (better than geom_point)
|
||||
geom_beeswarm(priority = "density"
|
||||
#, shape = 21
|
||||
, size = dot_size
|
||||
, alpha = dot_transparency
|
||||
, show.legend = FALSE
|
||||
, cex = 0.8
|
||||
, aes(colour = factor(eval(parse(text = colour_categ))) )) +
|
||||
|
||||
theme(axis.text.x = element_text(size = my_ats)
|
||||
, axis.text.y = element_text(size = my_ats
|
||||
, angle = 0
|
||||
|
|
@ -46,10 +71,15 @@ lf_bp_with_stats <- function(lf_df
|
|||
, vjust = 0)
|
||||
, axis.title.x = element_text(size = my_ats)
|
||||
, axis.title.y = element_text(size = my_ats)
|
||||
, plot.title = element_text(size = my_pts , hjust = 0.5, colour = "black", face = "bold")
|
||||
, plot.title = element_text(size = my_pts
|
||||
, hjust = 0.5
|
||||
, colour = "black"
|
||||
, face = "bold")
|
||||
, strip.background = element_rect(fill = colour_bp_strip)
|
||||
, strip.text.x = element_text(size = my_fls, colour = "black")
|
||||
, legend.title = element_text(color = "black", size = my_als)
|
||||
, strip.text.x = element_text(size = my_fls
|
||||
, colour = "black")
|
||||
, legend.title = element_text(color = "black"
|
||||
, size = my_als)
|
||||
, legend.text = element_text(size = my_ats)
|
||||
, legend.direction = "vertical") +
|
||||
|
||||
|
|
@ -60,7 +90,6 @@ lf_bp_with_stats <- function(lf_df
|
|||
stat_compare_means(comparisons = my_comparisonsL
|
||||
, method = stat_method
|
||||
, paired = my_paired
|
||||
#, label = "p.format")
|
||||
, label = stat_label[1])
|
||||
|
||||
return(bp_statP)
|
||||
83
scripts/functions/redundant/test_lf_bp_with_stats.R
Normal file
83
scripts/functions/redundant/test_lf_bp_with_stats.R
Normal file
|
|
@ -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)
|
||||
55
scripts/functions/test_lf_bp.R
Normal file
55
scripts/functions/test_lf_bp.R
Normal file
|
|
@ -0,0 +1,55 @@
|
|||
setwd("~/git/LSHTM_analysis/scripts/plotting/")
|
||||
source("Header_TT.R")
|
||||
source("../functions/lf_bp.R")
|
||||
# ================================================
|
||||
# Data: run get_plotting_data.R
|
||||
# to get the long format data to test this function
|
||||
# drug = "streptomycin"
|
||||
# gene = "gid"
|
||||
# source("get_plotting_dfs.R")
|
||||
# ==================================================
|
||||
|
||||
######################
|
||||
# Make plot: ggplot
|
||||
######################
|
||||
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") )
|
||||
|
||||
######################
|
||||
# Make plot: plotly
|
||||
######################
|
||||
# FIXME: This labels are not working as I want!
|
||||
# lf_bp_plotly(lf_df = lf_deepddg
|
||||
# , p_title = "DeepDDG"
|
||||
# , colour_categ = "deepddg_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)
|
||||
# )
|
||||
|
|
@ -1,28 +0,0 @@
|
|||
setwd("~/git/LSHTM_analysis/scripts/plotting/")
|
||||
|
||||
source("../functions/lf_bp_with_stats.R")
|
||||
|
||||
######################
|
||||
# call function
|
||||
######################
|
||||
# Note: Data
|
||||
# run other_plots_data.R
|
||||
# to get the long format data to test this function
|
||||
|
||||
lf_bp_with_stats(lf_df = lf_dynamut2
|
||||
, x_grp = "mutation_info"
|
||||
, y_var = "param_value"
|
||||
, facet_var = "param_type"
|
||||
, n_facet_row = 1
|
||||
, y_scales = "free_y"
|
||||
, p_title = "Dynamut2"
|
||||
, colour_categ = "ddg_dynamut2_outcome"
|
||||
, stat_grp_comp = c("DM", "OM")
|
||||
, stat_method = "wilcox.test"
|
||||
, my_paired = FALSE
|
||||
#, stat_label = "p.format")
|
||||
, stat_label = c("p.format", "p.signif")
|
||||
, my_ats = 22 # axis text size
|
||||
, my_als = 20 # axis label size
|
||||
, my_fls = 20 # facet label size
|
||||
, my_pts = 22 )# plot title size
|
||||
Loading…
Add table
Add a link
Reference in a new issue