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renamed 2 to _v2

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This commit is contained in:
Tanushree Tunstall 2022-08-22 11:41:42 +01:00
parent c9d7ea9fad
commit 802d6f8495
18 changed files with 761 additions and 976 deletions
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74
config/gid.R
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@ -17,7 +17,7 @@ aa_ligplus_sam = c(148, 137, 138, 139
, 93, 69, 119, 120
, 220, 219, 118, 223)
aa_ligplus_sam_hbond = c(220, 223)
aa_ligplus_amp = c(123, 125, 213, 214)
aa_ligplus_amp_hbond = c(125, 123, 213)
@ -53,19 +53,19 @@ aa_arpeg_amp = c(123, 125, 213)
# Active site
#=============
active_aa_pos = sort(unique(c(
#rna_bind_aa_pos
#, binding_aa_pos
aa_ligplus_sry
, aa_ligplus_sam
, aa_ligplus_amp
, aa_ligplus_rna
, aa_plip_sry
, aa_plip_sam
, aa_plip_amp
, aa_plip_rna
, aa_arpeg_sry
, aa_arpeg_sam
, aa_arpeg_amp
#rna_bind_aa_pos
#, binding_aa_pos
aa_ligplus_sry
, aa_ligplus_sam
, aa_ligplus_amp
, aa_ligplus_rna
, aa_plip_sry
, aa_plip_sam
, aa_plip_amp
, aa_plip_rna
, aa_arpeg_sry
, aa_arpeg_sam
, aa_arpeg_amp
)))
##############################################################
@ -77,42 +77,42 @@ cat("\nNo. of active site residues for gene"
##############################################################
aa_pos_sry = sort(unique(c(
aa_ligplus_sry
, aa_plip_sry
, aa_arpeg_sry)))
aa_ligplus_sry
, aa_plip_sry
, aa_arpeg_sry)))
aa_pos_drug = aa_pos_sry
aa_pos_sry_hbond = sort(unique(c(
aa_ligplus_sry_hbond
, aa_plip_sry_hbond)))
aa_ligplus_sry_hbond
, aa_plip_sry_hbond)))
aa_pos_rna = sort(unique(c(
aa_ligplus_rna
, aa_plip_rna)))
aa_ligplus_rna
, aa_plip_rna)))
aa_pos_rna_hbond = sort(unique(c(
aa_ligplus_rna_hbond
, aa_plip_rna_hbond)))
aa_ligplus_rna_hbond
, aa_plip_rna_hbond)))
aa_pos_sam = sort(unique(c(
aa_ligplus_sam
, aa_plip_sam
, aa_arpeg_sam)))
aa_ligplus_sam
, aa_plip_sam
, aa_arpeg_sam)))
aa_pos_sam_hbond = sort(unique(c(
aa_ligplus_sam_hbond
, aa_plip_sam_hbond)))
aa_ligplus_sam_hbond
, aa_plip_sam_hbond)))
aa_pos_amp = sort(unique(c(
aa_ligplus_amp
, aa_plip_amp
, aa_arpeg_amp)))
aa_ligplus_amp
, aa_plip_amp
, aa_arpeg_amp)))
aa_pos_amp_hbond = sort(unique(c(
aa_ligplus_amp_hbond
, aa_plip_amp_hbond)))
aa_ligplus_amp_hbond
, aa_plip_amp_hbond)))
cat("\n==================================================="
@ -129,9 +129,11 @@ cat("\n==================================================="
##############################################################
# var for position customisation for plots
aa_pos_lig1 = aa_pos_rna
aa_pos_lig2 = aa_pos_sam
aa_pos_drug
aa_pos_lig1 = aa_pos_sam
aa_pos_lig2 = aa_pos_rna
aa_pos_lig3 = aa_pos_amp
tile_map=data.frame(tile=c("GID","DPA","CDL","Ca"),
tile_map=data.frame(tile=c("SRY","SAM","RNA","AMP"),
tile_colour=c("green","darkslategrey","navyblue","purple"))