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lineage dist plots combined generated

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Tanushree Tunstall 2020-09-09 13:18:57 +01:00
parent 19a984f228
commit 080cd6375d
2 changed files with 27 additions and 9 deletions
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17
scripts/plotting/lineage_dist_PS.R
View file

@ -1,8 +1,4 @@
#!/usr/bin/env Rscript #!/usr/bin/env Rscript
getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd()
######################################################### #########################################################
# TASK: Lineage dist plots: ggridges # TASK: Lineage dist plots: ggridges
@ -14,7 +10,12 @@ getwd()
########################################################## ##########################################################
# Installing and loading required packages # Installing and loading required packages
########################################################## ##########################################################
getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/")
getwd()
source("Header_TT.R")
library(ggridges)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
# PS combined: # PS combined:
# 1) merged_df2 # 1) merged_df2
@ -273,9 +274,9 @@ p2 = ggplot(df_dr, aes(x = duet_scaled
, axis.ticks.y = element_blank() , axis.ticks.y = element_blank()
, plot.title = element_blank() , plot.title = element_blank()
, strip.text = element_text(size = my_als) , strip.text = element_text(size = my_als)
#, legend.text = element_text(size = 10) , legend.text = element_text(size = 10)
#, legend.title = element_text(size = my_als) , legend.title = element_text(size = my_als)
, legend.position = "none" #, legend.position = "none"
) )
print(p2) print(p2)
@ -288,7 +289,7 @@ print(p2)
lineage_dist_combined = "lineage_dist_combined_PS.svg" lineage_dist_combined = "lineage_dist_combined_PS.svg"
plot_lineage_dist_combined = paste0(plotdir,"/", lineage_dist_combined) plot_lineage_dist_combined = paste0(plotdir,"/", lineage_dist_combined)
svg(plot_lineage_dist_combined, width = 16, height = 12) svg(plot_lineage_dist_combined, width = 12, height = 6)
printFile = cowplot::plot_grid(p1, p2 printFile = cowplot::plot_grid(p1, p2
, label_size = my_als+10) , label_size = my_als+10)

17
scripts/plotting/running_plot_scripts
View file

@ -3,6 +3,9 @@
#======== #========
FIXME: FIXME:
#=======================
dirs.R
#=======================
#dirs.R: imports dir structure #dirs.R: imports dir structure
change this to cmd so you can pass in drug and gene name change this to cmd so you can pass in drug and gene name
@ -11,6 +14,13 @@ plotting_data.R
#======================= #=======================
??? update how to run ??? update how to run
#=======================
combining_dfs_plotting.R
#=======================
??? update how to run
#======================= #=======================
mcsm_mean_stability.R mcsm_mean_stability.R
#======================= #=======================
@ -62,6 +72,13 @@ barplots_subcolours_PS.R
# output plots: 1 svg # output plots: 1 svg
1) barplot_coloured_PS.svg 1) barplot_coloured_PS.svg
#=======================
lineage_dist_PS.R
# lineage distribution for all muts and dr muts in one figure
#=======================
# input: calls the "combining_dfs_plotting.R"
# output plots: 1 svg
1) lineage_dist_combined_PS.svg
######################################################################## ########################################################################