tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

multiple script updates and bug fixes

Browse source
This commit is contained in:
Tanushree Tunstall 2022-08-04 16:48:17 +01:00
parent 599cd7493f
commit bf41d01b39
2 changed files with 13 additions and 8 deletions
Download patch file Download diff file Expand all files Collapse all files

19
scripts/functions/corr_plot_data.R
View file

@ -25,7 +25,7 @@
corr_data_extract <- function(df
#, gene_name = gene
, drug_name = drug
, ligand_dist_colname = LigDist_colname
#, ligand_dist_colname = LigDist_colname
, colnames_to_extract
, colnames_display_key
, extract_scaled_cols = F){
@ -43,11 +43,13 @@ corr_data_extract <- function(df
colnames_to_extract = c(drug
#, "mutationinformation"
, "mutation_info_labels"
#, "mutation_info_labels"
, "dst_mode"
, "duet_stability_change"
, "ligand_affinity_change"
#, "ligand_distance"
, ligand_dist_colname
, "ligand_distance"
#, ligand_dist_colname
, "interface_dist"
, "ddg_foldx"
, "deepddg"
, "asa"
@ -80,8 +82,9 @@ corr_data_extract <- function(df
# arg: colnames_display_key
colnames_display_key = c(duet_stability_change = "DUET"
, ligand_affinity_change = "mCSM-lig"
#, ligand_distance = "ligand_distance"
, ligand_distance = "ligand_distance"
#, ligand_dist_colname = "ligand_distance"
, interface_dist = "interface_dist"
, ddg_foldx = "FoldX"
, deepddg = "DeepDDG"
, asa = "ASA"
@ -122,9 +125,11 @@ corr_data_extract <- function(df
# Move drug column to the end
last_col = colnames(corr_df[ncol(corr_df)])
corr_df_f = corr_df %>% dplyr::relocate(all_of(drug), .after = last_col)
#corr_df_f = corr_df %>% dplyr::relocate(all_of(drug), .after = last_col)
#return(corr_df_f)
return(corr_df)
return(corr_df_f)
}
}

2
scripts/functions/my_pairs_panel.R
View file

@ -12,7 +12,7 @@ my_corr_pairs <- function (corr_data_all
{
corr_data_df = corr_data_all[corr_cols]
my_bg = categ_colour[corr_data_all[[colour_categ_col]] ]
my_bg = categ_colour[as.factor(corr_data_all[[colour_categ_col]])] # converted to factor
OutPlot_corr = pairs.panels(corr_data_df
, method = corr_method