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gg pairs fixup for alr

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Tanushree Tunstall 2022-08-27 17:15:31 +01:00
parent 5b89beb2b5
commit c3067b9176
1 changed files with 43 additions and 25 deletions
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68
scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R
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@ -1,6 +1,6 @@
#source("~/git/LSHTM_analysis/config/embb.R") #source("~/git/LSHTM_analysis/config/alr.R")
#source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") #source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
#======= #=======
# output # output
@ -8,20 +8,38 @@
outdir_images = paste0("/home/pub/Work/LSHTM/Thesis_Plots/pairs/") outdir_images = paste0("/home/pub/Work/LSHTM/Thesis_Plots/pairs/")
#cat("plots will output to:", outdir_images) #cat("plots will output to:", outdir_images)
custom_cor <- function(data, mapping, method, ...){
x <- eval_data_col(data, mapping$x)
y <- eval_data_col(data, mapping$y)
corr <- cor(x, y, method=method, use='complete.obs')
ggally_text(
label = paste0("ρ: ",as.character(round(corr, 2))),
mapping = aes(),
xP = 0.5, yP = 0.5,
color = 'black',
...
)
}
my_gg_pairs=function(plot_df, plot_title my_gg_pairs=function(plot_df, plot_title
, tt_args_size = 2.5 , tt_args_size = 2.5
, gp_args_size = 2.5){ , gp_args_size = 2.5){
ggpairs(plot_df, ggpairs(plot_df,
columns = 1:(ncol(plot_df)-1), columns = 1:(ncol(plot_df)-1),
upper = list( upper = list(
continuous = wrap('cor', # ggally_cor() continuous = wrap(custom_cor, method="spearman"
method = "spearman", # ggally_cor, # ggally_cor()
use = "pairwise.complete.obs", # method = "spearman",
title="ρ", # use = "pairwise.complete.obs",
digits=2, # title="XXX ρ",
justify_labels = "centre", # digits=2,
title_args=list(size=tt_args_size, colour="black")#,#2.5 # justify_labels = "centre",
#group_args=list(size=gp_args_size)#2.5 # title_args=list(size=tt_args_size, colour="black")#,#2.5
# #group_args=list(size=gp_args_size)#2.5
) )
), ),
lower = list( lower = list(
@ -29,22 +47,22 @@ my_gg_pairs=function(plot_df, plot_title
"points", "points",
alpha = 0.7, alpha = 0.7,
size=0.125 size=0.125
),
combo = wrap(
"dot",
alpha = 0.7,
size=0.125)
), ),
combo = wrap( # aes(colour = factor(ifelse(dst_mode==0,
"dot", # "S",
alpha = 0.7, # "R") ),
size=0.125) # alpha = 0.5),
), title=plot_title) #+
# aes(colour = factor(ifelse(dst_mode==0, #
# "S", # scale_colour_manual(values = c("red", "blue")) +
# "R") ), # scale_fill_manual(values = c("red", "blue")) #+
# alpha = 0.5), # theme(text = element_text(size=7,
title=plot_title) #+ # face="bold"))
#
# scale_colour_manual(values = c("red", "blue")) +
# scale_fill_manual(values = c("red", "blue")) #+
# theme(text = element_text(size=7,
# face="bold"))
} }
DistCutOff = 10 DistCutOff = 10