saving previous stuff from work
This commit is contained in:
parent
c10d54f104
commit
29022c5462
2 changed files with 18 additions and 198 deletions
|
|
@ -1,203 +1,23 @@
|
|||
getwd()
|
||||
setwd("~/git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts/plotting")
|
||||
getwd()
|
||||
source("../combining_two_df.R")
|
||||
source("../Header_TT.R")
|
||||
getwd()
|
||||
setwd("~/git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts/plotting")
|
||||
getwd()
|
||||
source("../Header_TT.R")
|
||||
source("../barplot_colour_function.R")
|
||||
############################################################
|
||||
# Output dir for plots
|
||||
############################################################
|
||||
out_dir = "~/git/Data/pyrazinamide/output/plots"
|
||||
source("subcols_axis.R")
|
||||
table(mut_pos_cols$lab_bg)
|
||||
#blue cornflowerblue green purple white yellow
|
||||
#2 2 2 4 117 3
|
||||
sum( table(mut_pos_cols$lab_bg) ) == nrow(mut_pos_cols) # should be True
|
||||
table(mut_pos_cols$lab_bg2)
|
||||
#green white
|
||||
#2 128
|
||||
sum( table(mut_pos_cols$lab_bg2) ) == nrow(mut_pos_cols) # should be True
|
||||
table(mut_pos_cols$lab_fg)
|
||||
#black white
|
||||
#124 6
|
||||
sum( table(mut_pos_cols$lab_fg) ) == nrow(mut_pos_cols) # should be True
|
||||
# very important!
|
||||
my_axis_colours = mut_pos_cols$lab_fg
|
||||
# now clear mut_pos_cols
|
||||
rm(mut_pos_cols)
|
||||
###########################
|
||||
# 2: Plot: DUET scores
|
||||
###########################
|
||||
#==========================
|
||||
# Plot 2: Barplot with scores (unordered)
|
||||
# corresponds to DUET_outcome
|
||||
# Stacked Barplot with colours: DUET_outcome @ position coloured by
|
||||
# stability scores. This is a barplot where each bar corresponds
|
||||
# to a SNP and is coloured by its corresponding DUET stability value.
|
||||
# Normalised values (range between -1 and 1 ) to aid visualisation
|
||||
# NOTE: since barplot plots discrete values, colour = score, so number of
|
||||
# colours will be equal to the no. of unique normalised scores
|
||||
# rather than a continuous scale
|
||||
# will require generating the colour scale separately.
|
||||
#============================
|
||||
# sanity checks
|
||||
upos = unique(my_df$Position)
|
||||
str(my_df$DUET_outcome)
|
||||
colnames(my_df)
|
||||
#===========================
|
||||
# Data preparation for plots
|
||||
#===========================
|
||||
#!!!!!!!!!!!!!!!!!
|
||||
source("../combining_two_df.R")
|
||||
#<<<<<<<<<<<<<<<<<<<<<<<<<
|
||||
# REASSIGNMENT
|
||||
df <- my_df
|
||||
#!!!!!!!!!!!!!!!!!
|
||||
my_df = merged_df3_comp
|
||||
# delete variables not required
|
||||
rm(merged_df2, merged_df2_comp, merged_df3, merged_df3_comp)
|
||||
# quick checks
|
||||
colnames(my_df)
|
||||
str(my_df)
|
||||
#<<<<<<<<<<<<<<<<<<<<<<<<
|
||||
# REASSIGNMENT
|
||||
df = my_df
|
||||
rm(my_df)
|
||||
# sanity checks
|
||||
# should be a factor
|
||||
is.factor(df$DUET_outcome)
|
||||
#TRUE
|
||||
table(df$DUET_outcome)
|
||||
#Destabilizing Stabilizing
|
||||
#288 47
|
||||
# should be -1 and 1
|
||||
min(df$ratioDUET)
|
||||
max(df$ratioDUET)
|
||||
# sanity checks
|
||||
# very important!!!!
|
||||
tapply(df$ratioDUET, df$DUET_outcome, min)
|
||||
#Destabilizing Stabilizing
|
||||
#-1.0000000 0.01065719
|
||||
tapply(df$ratioDUET, df$DUET_outcome, max)
|
||||
#Destabilizing Stabilizing
|
||||
#-0.003875969 1.0000000
|
||||
# check unique values in normalised data
|
||||
u = unique(df$ratioDUET) # 323
|
||||
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
# Run this section if rounding is to be used
|
||||
# specify number for rounding
|
||||
n = 3
|
||||
df$ratioDUETR = round(df$ratioDUET, n) # 335, 40
|
||||
u = unique(df$ratioDUETR) # 287
|
||||
# create an extra column called group which contains the "gp name and score"
|
||||
# so colours can be generated for each unique values in this column
|
||||
my_grp = df$ratioDUETR
|
||||
df$group <- paste0(df$DUET_outcome, "_", my_grp, sep = "") # 335,41
|
||||
# Call the function to create the palette based on the group defined above
|
||||
colours <- ColourPalleteMulti(df, "DUET_outcome", "my_grp")
|
||||
my_title = "Protein stability (DUET)"
|
||||
library(ggplot2)
|
||||
# axis label size
|
||||
my_xaxls = 13
|
||||
my_yaxls = 15
|
||||
# axes text size
|
||||
my_xaxts = 15
|
||||
my_yaxts = 15
|
||||
# no ordering of x-axis according to frequency
|
||||
g = ggplot(df, aes(factor(Position, ordered = T)))
|
||||
g +
|
||||
geom_bar(aes(fill = group), colour = "grey") +
|
||||
scale_fill_manual( values = colours
|
||||
, guide = 'none') +
|
||||
theme( axis.text.x = element_text(size = my_xaxls
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
, axis.text.y = element_text(size = my_yaxls
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_text(size = my_xaxts)
|
||||
, axis.title.y = element_text(size = my_yaxts ) ) +
|
||||
labs(title = my_title
|
||||
, x = "Position"
|
||||
, y = "Frequency")
|
||||
class(df$lab_bg)
|
||||
# make this a named vector
|
||||
# define cartesian coord
|
||||
my_xlim = length(unique(df$Position)); my_xlim
|
||||
# axis label size
|
||||
my_xals = 15
|
||||
my_yals = 15
|
||||
# axes text size
|
||||
my_xats = 15
|
||||
my_yats = 18
|
||||
# using geom_tile
|
||||
g = ggplot(df, aes(factor(Position, ordered = T)))
|
||||
g +
|
||||
coord_cartesian(xlim = c(1, my_xlim)
|
||||
, ylim = c(0, 6)
|
||||
, clip = "off") +
|
||||
geom_bar(aes(fill = group), colour = "grey") +
|
||||
scale_fill_manual( values = colours
|
||||
, guide = 'none') +
|
||||
geom_tile(aes(,-0.8, width = 0.9, height = 0.85)
|
||||
, fill = df$lab_bg) +
|
||||
geom_tile(aes(,-1.2, width = 0.9, height = -0.2)
|
||||
, fill = df$lab_bg2) +
|
||||
# Here it's important to specify that your axis goes from 1 to max number of levels
|
||||
theme( axis.text.x = element_text(size = my_xats
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4
|
||||
, colour = my_axis_colours)
|
||||
, axis.text.y = element_text(size = my_yats
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_text(size = my_xals)
|
||||
, axis.title.y = element_text(size = my_yals )
|
||||
, axis.ticks.x = element_blank()
|
||||
) +
|
||||
labs(title = my_title
|
||||
, x = "Position"
|
||||
, y = "Frequency")
|
||||
class(df$lab_bg)
|
||||
# make this a named vector
|
||||
# define cartesian coord
|
||||
my_xlim = length(unique(df$Position)); my_xlim
|
||||
# axis label size
|
||||
my_xals = 18
|
||||
my_yals = 18
|
||||
# axes text size
|
||||
my_xats = 14
|
||||
my_yats = 18
|
||||
my_plot_name = "barplot_PS_acoloured.svg"
|
||||
out_file = paste0(out_dir, "/", my_plot_name); outfile
|
||||
svg(outfile, width = 26, height = 4)
|
||||
svg(out_file, width = 26, height = 4)
|
||||
# using geom_tile
|
||||
g = ggplot(df, aes(factor(Position, ordered = T)))
|
||||
outFile = g +
|
||||
coord_cartesian(xlim = c(1, my_xlim)
|
||||
, ylim = c(0, 6)
|
||||
, clip = "off"
|
||||
) +
|
||||
geom_bar(aes(fill = group), colour = "grey") +
|
||||
scale_fill_manual( values = colours
|
||||
, guide = 'none') +
|
||||
# geom_tile(aes(,-0.6, width = 0.9, height = 0.7)
|
||||
# , fill = df$lab_bg) +
|
||||
# geom_tile(aes(,-1, width = 0.9, height = 0.3)
|
||||
# , fill = df$lab_bg2) +
|
||||
geom_tile(aes(,-0.8, width = 0.9, height = 0.85)
|
||||
, fill = df$lab_bg) +
|
||||
geom_tile(aes(,-1.2, width = 0.9, height = -0.2)
|
||||
, fill = df$lab_bg2) +
|
||||
# Here it's important to specify that your axis goes from 1 to max number of levels
|
||||
theme( axis.text.x = element_text(size = my_xats
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4
|
||||
, colour = my_axis_colours)
|
||||
, axis.text.y = element_text(size = my_yats
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_text(size = my_xals)
|
||||
, axis.title.y = element_text(size = my_yals )
|
||||
, axis.ticks.x = element_blank()
|
||||
) +
|
||||
labs(title = ""
|
||||
, x = "Position"
|
||||
, y = "Frequency")
|
||||
print(outFile)
|
||||
dev.off()
|
||||
|
|
|
|||
|
|
@ -64,10 +64,10 @@ str(my_df)
|
|||
# Data for plots
|
||||
#===================
|
||||
|
||||
#<<<<<<<<<<<<<<<<<<<<<<<<
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
# REASSIGNMENT
|
||||
df = my_df
|
||||
#<<<<<<<<<<<<<<<<<<<<<<<<<
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
|
||||
rm(my_df)
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue