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Tanushree Tunstall 2022-08-15 20:39:35 +01:00
parent 0cc7a8fcae
commit 2e29cf8011
3 changed files with 19 additions and 11 deletions
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2
config/pnca.R
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@ -52,6 +52,8 @@ cat("\n==================================================="
############################################################## ##############################################################
# var for position customisation for plots # var for position customisation for plots
aa_pos_lig1 = aa_pos_fe aa_pos_lig1 = aa_pos_fe
aa_pos_lig2 = NULL
aa_pos_lig3 = NULL
#aa_pos_lig2 = aa_pos_catalytic #aa_pos_lig2 = aa_pos_catalytic
#aa_pos_lig3 = aa_pos_hbond #aa_pos_lig3 = aa_pos_hbond
tile_map=data.frame(tile=c("PZA","DSL","CDL","Ca"), tile_map=data.frame(tile=c("PZA","DSL","CDL","Ca"),

5
scripts/functions/bp_subcolours.R
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@ -97,8 +97,9 @@ bp_stability_hmap <- function(plot_df = merged_df3
# Generate the subcols barplot # Generate the subcols barplot
cowplot::plot_grid( cowplot::plot_grid(
ggplot(plot_df, aes_string(x = xvar_colname ggplot(plot_df, aes_string(x = xvar_colname
# , ordered = T) #, ordered = T
)) + )
) +
geom_bar(aes(fill = group) geom_bar(aes(fill = group)
, colour = "grey", size=0.125) + , colour = "grey", size=0.125) +

23
scripts/functions/logoP_snp.R
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@ -37,8 +37,8 @@ LogoPlotSnps <- function(plot_df
, omit_snp_count = c(0) # can be 1, 2, etc. , omit_snp_count = c(0) # can be 1, 2, etc.
, my_logo_col = "chemistry" , my_logo_col = "chemistry"
, x_lab = "Position" , x_lab = "Position"
, y_lab = "Count" , y_lab = "nsSNP Count"
, x_ats = 7 # text size , x_ats = 6 # text size
, x_tangle = 90 # text angle , x_tangle = 90 # text angle
, y_ats = 10 , y_ats = 10
, y_tangle = 0 , y_tangle = 0
@ -237,17 +237,21 @@ LogoPlotSnps <- function(plot_df
, colour = xfont_bgc , colour = xfont_bgc
#, margin = margin(t = 0.1) #, margin = margin(t = 0.1)
) )
, axis.text.y = element_text(size = y_ats , axis.text.y = element_blank()
, angle = y_tangle # , axis.text.y = element_text(size = y_ats
, hjust = 1 # , angle = y_tangle
, vjust = -1.0 # , hjust = 1
, colour = yfont_bgc) # , vjust = -1.0
# , colour = yfont_bgc)
# , axis.title.x = element_text(size = x_tts # , axis.title.x = element_text(size = x_tts
# , colour = xtt_col) # , colour = xtt_col)
, axis.title.x = element_blank() , axis.title.x = element_blank()
, axis.title.y = element_text(size = y_tts , axis.title.y = element_text(size = y_tts
, angle = 90 , angle = 90
, colour = ytt_col) , colour = ytt_col
, margin = margin(t = 0, r = 0, b = 20, l = 0)
#, hjust = -2
)
, plot.background = element_rect(fill = theme_bgc, colour=NA) , plot.background = element_rect(fill = theme_bgc, colour=NA)
) + ) +
@ -269,11 +273,12 @@ LogoPlotSnps <- function(plot_df
, legend.position = "none" , legend.position = "none"
, axis.text.x = element_blank() , axis.text.x = element_blank()
, axis.text.y = element_blank() , axis.text.y = element_blank()
#, axis.text.y = element_text()
, axis.title.x = element_blank() , axis.title.x = element_blank()
, axis.title.y = element_blank() , axis.title.y = element_blank()
, plot.background = element_rect(fill = theme_bgc, colour=NA) , plot.background = element_rect(fill = theme_bgc, colour=NA)
) + ) +
labs(x=NULL, y=NULL) labs(x=NULL, y="WT")
anno_bar = position_annotation(plot_df, anno_bar = position_annotation(plot_df,
bg = theme_bgc, bg = theme_bgc,