consurf plot: add debug option. logoP SNP: distance flame tiles
This commit is contained in:
parent
f2709f3992
commit
e498d46f8b
2 changed files with 230 additions and 219 deletions
|
|
@ -13,99 +13,100 @@
|
|||
# input args
|
||||
#==========================================================
|
||||
wideP_consurf <- function(plotdf
|
||||
, xvar_colname = "position"
|
||||
, yvar_colname = "consurf_score"
|
||||
, yvar_colourN_colname = "consurf_colour_rev" # num from 0-1
|
||||
, plot_error_bars = T
|
||||
, upper_EB_colname = "consurf_ci_upper"
|
||||
, lower_EB_colname = "consurf_ci_lower"
|
||||
, xvar_colname = "position"
|
||||
, yvar_colname = "consurf_score"
|
||||
, yvar_colourN_colname = "consurf_colour_rev" # num from 0-1
|
||||
, plot_error_bars = T
|
||||
, upper_EB_colname = "consurf_ci_upper"
|
||||
, lower_EB_colname = "consurf_ci_lower"
|
||||
|
||||
, plot_type = "point" # default is point
|
||||
, point_colours
|
||||
, p_size = 2
|
||||
, leg_title1 = ""
|
||||
, leg_labels = c("0": "Insufficient Data"
|
||||
, "1": "Variable"
|
||||
, "2", "3", "4", "5", "6", "7", "8"
|
||||
, "9": "Conserved")
|
||||
, panel_col = "black"
|
||||
, panel_col_fill = "black"
|
||||
, plot_type = "point" # default is point
|
||||
, point_colours
|
||||
, p_size = 2
|
||||
, leg_title1 = ""
|
||||
, leg_labels = c("0": "Insufficient Data"
|
||||
, "1": "Variable"
|
||||
, "2", "3", "4", "5", "6", "7", "8"
|
||||
, "9": "Conserved")
|
||||
, panel_col = "black"
|
||||
, panel_col_fill = "black"
|
||||
|
||||
# axes title and label sizes
|
||||
, x_axls = 12 # x-axis label size
|
||||
, y_axls = 15 # y-axis label size
|
||||
, x_axts = 12 # x-axis text size
|
||||
, y_axts = 12 # y-axis text size
|
||||
, default_xtc = "black" # x-axis text colour
|
||||
, ptitle = ""
|
||||
, xlab = ""
|
||||
, ylab = ""
|
||||
, pts = 20
|
||||
# axes title and label sizes
|
||||
, x_axls = 12 # x-axis label size
|
||||
, y_axls = 15 # y-axis label size
|
||||
, x_axts = 12 # x-axis text size
|
||||
, y_axts = 12 # y-axis text size
|
||||
, default_xtc = "black" # x-axis text colour
|
||||
, ptitle = ""
|
||||
, xlab = ""
|
||||
, ylab = ""
|
||||
, pts = 20
|
||||
|
||||
# plot margins
|
||||
, t_margin = 0.5
|
||||
, r_margin = 0.5
|
||||
, b_margin = 1
|
||||
, l_margin = 1
|
||||
, unit_margin = "cm"
|
||||
# plot margins
|
||||
, t_margin = 0.5
|
||||
, r_margin = 0.5
|
||||
, b_margin = 1
|
||||
, l_margin = 1
|
||||
, unit_margin = "cm"
|
||||
|
||||
# Custom 1: x-axis: text colour
|
||||
, xtext_colour_aa = F
|
||||
, xtext_colour_aa1 = active_aa_pos
|
||||
, xtext_colour_aa2 = aa_pos_drug
|
||||
, xtext_colours = c("purple", "brown", "black")
|
||||
# Custom 1: x-axis: text colour
|
||||
, xtext_colour_aa = F
|
||||
, xtext_colour_aa1 = active_aa_pos
|
||||
, xtext_colour_aa2 = aa_pos_drug
|
||||
, xtext_colours = c("purple", "brown", "black")
|
||||
|
||||
# Custom 2: x-axis: geom tiles ~ lig distance
|
||||
, A_xvar_lig = T
|
||||
, leg_title2 = "Ligand Distance"
|
||||
, lig_dist_colname = LigDist_colname # from globals
|
||||
, lig_dist_colours = c("green", "yellow", "orange", "red")
|
||||
, tpos0 = 0 # 0 is a magic number that does my sensible default
|
||||
, tW0 = 1
|
||||
, tH0 = 0.3
|
||||
# Custom 2: x-axis: geom tiles ~ lig distance
|
||||
, A_xvar_lig = T
|
||||
, leg_title2 = "Ligand Distance"
|
||||
, lig_dist_colname = LigDist_colname # from globals
|
||||
, lig_dist_colours = c("green", "yellow", "orange", "red")
|
||||
, tpos0 = 0 # 0 is a magic number that does my sensible default
|
||||
, tW0 = 1
|
||||
, tH0 = 0.3
|
||||
|
||||
# Custom 3: x-axis: geom tiles ~ active sites and ligand
|
||||
, A_xvar_aa = F
|
||||
, aa_pos_drug = NULL
|
||||
, drug_aa_colour = "purple"
|
||||
, tW = 1
|
||||
, tH = 0.2
|
||||
, active_aa_pos = NULL
|
||||
, active_aa_colour = "brown"
|
||||
# Custom 3: x-axis: geom tiles ~ active sites and ligand
|
||||
, A_xvar_aa = F
|
||||
, aa_pos_drug = NULL
|
||||
, drug_aa_colour = "purple"
|
||||
, tW = 1
|
||||
, tH = 0.2
|
||||
, active_aa_pos = NULL
|
||||
, active_aa_colour = "brown"
|
||||
|
||||
, aa_pos_lig1 = NULL
|
||||
, aa_colour_lig1 = "blue"
|
||||
, tpos1 = 0
|
||||
, aa_pos_lig1 = NULL
|
||||
, aa_colour_lig1 = "blue"
|
||||
, tpos1 = 0
|
||||
|
||||
, aa_pos_lig2 = NULL
|
||||
, aa_colour_lig2 = "cyan"
|
||||
, tpos2 = 0
|
||||
, aa_pos_lig2 = NULL
|
||||
, aa_colour_lig2 = "cyan"
|
||||
, tpos2 = 0
|
||||
|
||||
, aa_pos_lig3 = NULL
|
||||
, aa_colour_lig3 = "cornflowerblue"
|
||||
, tpos3 = 0
|
||||
, aa_pos_lig3 = NULL
|
||||
, aa_colour_lig3 = "cornflowerblue"
|
||||
, tpos3 = 0
|
||||
|
||||
, default_gt_clr = "white"
|
||||
){
|
||||
, default_gt_clr = "white"
|
||||
, debug=FALSE
|
||||
){
|
||||
|
||||
if(missing(point_colours)){
|
||||
temp_cols = colorRampPalette(c("seagreen", "sienna3"))(30)
|
||||
point_colours = temp_cols
|
||||
}else{
|
||||
point_colours = point_colours
|
||||
}
|
||||
}else{
|
||||
point_colours = point_colours
|
||||
}
|
||||
|
||||
###############################
|
||||
# custom 1: x-axis text colour
|
||||
##############################
|
||||
|
||||
if (xtext_colour_aa){
|
||||
positionF <- levels(as.factor(plotdf[[xvar_colname]]))
|
||||
length(positionF)
|
||||
aa_pos_colours = ifelse(positionF%in%xtext_colour_aa1, xtext_colours[1]
|
||||
, ifelse(positionF%in%xtext_colour_aa2
|
||||
, xtext_colours[2]
|
||||
, xtext_colours[3]))
|
||||
positionF <- levels(as.factor(plotdf[[xvar_colname]]))
|
||||
length(positionF)
|
||||
aa_pos_colours = ifelse(positionF%in%xtext_colour_aa1, xtext_colours[1]
|
||||
, ifelse(positionF%in%xtext_colour_aa2
|
||||
, xtext_colours[2]
|
||||
, xtext_colours[3]))
|
||||
}else{
|
||||
aa_pos_colours = default_xtc
|
||||
}
|
||||
|
|
@ -170,9 +171,9 @@ wideP_consurf <- function(plotdf
|
|||
, ligD = plotdf[[lig_dist_colname]]
|
||||
, ligDR = plotdf$lig_distR
|
||||
, ligD_cols = plotdf$ligD_colours))
|
||||
} else{
|
||||
plotdf = plotdf
|
||||
}
|
||||
} else{
|
||||
plotdf = plotdf
|
||||
}
|
||||
|
||||
###############################################
|
||||
# Custom 3: x-axis geom tiles ~ active sites
|
||||
|
|
@ -249,9 +250,9 @@ wideP_consurf <- function(plotdf
|
|||
# , colour = y_colour_factor)
|
||||
|
||||
g = ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
|
||||
, y = yvar_colname
|
||||
, colour = sprintf("factor(%s)", yvar_colourN_colname)
|
||||
))
|
||||
, y = yvar_colname
|
||||
, colour = sprintf("factor(%s)", yvar_colourN_colname)
|
||||
))
|
||||
# g = ggplot(plotdf, aes_string(x = "position")
|
||||
# , y = "consurf_score"
|
||||
# , colour = "consurf_colour_rev")
|
||||
|
|
@ -273,19 +274,19 @@ wideP_consurf <- function(plotdf
|
|||
, ylim = c(ymin, ymax)
|
||||
, clip = "off") +
|
||||
geom_point(size = p_size) +
|
||||
scale_colour_manual(values = point_colours)
|
||||
# , labels = leg_labels
|
||||
# , name = leg_title1)
|
||||
scale_colour_manual(values = point_colours)
|
||||
# , labels = leg_labels
|
||||
# , name = leg_title1)
|
||||
}
|
||||
|
||||
if (plot_error_bars){
|
||||
g0 = g0 +
|
||||
geom_errorbar(aes(ymin = eval(parse(text = lower_EB_colname))
|
||||
, ymax = eval(parse(text = upper_EB_colname))
|
||||
))
|
||||
}else{
|
||||
, ymax = eval(parse(text = upper_EB_colname))
|
||||
))
|
||||
}else{
|
||||
|
||||
g0 = g0
|
||||
g0 = g0
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -298,22 +299,22 @@ wideP_consurf <- function(plotdf
|
|||
, vjust = 0.4
|
||||
, face = "bold"
|
||||
, colour = aa_pos_colours)
|
||||
, axis.text.y = element_text(size = y_axts
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_text(size = x_axls)
|
||||
, axis.title.y = element_text(size = y_axls )
|
||||
, panel.background = element_rect(fill = panel_col_fill, color = panel_col)
|
||||
, panel.grid.major = element_line(color = "black")
|
||||
, panel.grid.minor = element_line(color = "black")
|
||||
, plot.title = element_text(size = pts
|
||||
, hjust = 0.5)
|
||||
, plot.margin = margin(t = t_margin
|
||||
, r = r_margin
|
||||
, b = b_margin
|
||||
, l = l_margin
|
||||
, unit = unit_margin))+
|
||||
, axis.text.y = element_text(size = y_axts
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_text(size = x_axls)
|
||||
, axis.title.y = element_text(size = y_axls )
|
||||
, panel.background = element_rect(fill = panel_col_fill, color = panel_col)
|
||||
, panel.grid.major = element_line(color = "black")
|
||||
, panel.grid.minor = element_line(color = "black")
|
||||
, plot.title = element_text(size = pts
|
||||
, hjust = 0.5)
|
||||
, plot.margin = margin(t = t_margin
|
||||
, r = r_margin
|
||||
, b = b_margin
|
||||
, l = l_margin
|
||||
, unit = unit_margin))+
|
||||
guides(colour = guide_legend(title = "ConsurfXXXX")) +
|
||||
|
||||
labs(title = ptitle
|
||||
|
|
@ -364,39 +365,39 @@ wideP_consurf <- function(plotdf
|
|||
g2 = g1 + geom_tile(aes(, tpos0
|
||||
, width = tW0
|
||||
, height = tH0)
|
||||
, fill = plotdf$ligD_colours
|
||||
, colour = plotdf$ligD_colours
|
||||
, linetype = "blank")
|
||||
, fill = plotdf$ligD_colours
|
||||
, colour = plotdf$ligD_colours
|
||||
, linetype = "blank")
|
||||
|
||||
#cat("Nrows of plot df", length(plotdf$ligD_colours))
|
||||
out = g2
|
||||
#
|
||||
# #------------------
|
||||
# # Extract legend2
|
||||
# #------------------
|
||||
# labels = seq(lig_min, lig_max, len = 5); labels
|
||||
# labelsD = round(labels, digits = 0); labelsD
|
||||
#
|
||||
# g2_leg = g1 +
|
||||
# geom_tile(aes(fill = .data[[lig_dist_colname]])
|
||||
# , colour = "white") +
|
||||
# scale_fill_gradient2(midpoint = lig_mean
|
||||
# , low = "green"
|
||||
# , mid = "yellow"
|
||||
# , high = "red"
|
||||
# , breaks = labels
|
||||
# #, n.breaks = 11
|
||||
# #, minor_breaks = c(2, 4, 6, 8, 10)
|
||||
# , limits = c(lig_min, lig_max)
|
||||
# , labels = labelsD
|
||||
# , name = leg_title2)
|
||||
#
|
||||
# legend2 = get_legend(g2_leg)
|
||||
#
|
||||
# }else{
|
||||
# out = g1
|
||||
# }
|
||||
######################################################
|
||||
#
|
||||
# #------------------
|
||||
# # Extract legend2
|
||||
# #------------------
|
||||
# labels = seq(lig_min, lig_max, len = 5); labels
|
||||
# labelsD = round(labels, digits = 0); labelsD
|
||||
#
|
||||
# g2_leg = g1 +
|
||||
# geom_tile(aes(fill = .data[[lig_dist_colname]])
|
||||
# , colour = "white") +
|
||||
# scale_fill_gradient2(midpoint = lig_mean
|
||||
# , low = "green"
|
||||
# , mid = "yellow"
|
||||
# , high = "red"
|
||||
# , breaks = labels
|
||||
# #, n.breaks = 11
|
||||
# #, minor_breaks = c(2, 4, 6, 8, 10)
|
||||
# , limits = c(lig_min, lig_max)
|
||||
# , labels = labelsD
|
||||
# , name = leg_title2)
|
||||
#
|
||||
# legend2 = get_legend(g2_leg)
|
||||
#
|
||||
# }else{
|
||||
# out = g1
|
||||
# }
|
||||
######################################################
|
||||
#------------------
|
||||
# Extract legend2
|
||||
#------------------
|
||||
|
|
@ -404,7 +405,7 @@ wideP_consurf <- function(plotdf
|
|||
labelsD = round(labels, digits = 0); labelsD
|
||||
g2_leg = ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
|
||||
, y = yvar_colname)
|
||||
) +
|
||||
) +
|
||||
geom_tile(aes(fill = .data[[lig_dist_colname]])
|
||||
, colour = "white") +
|
||||
scale_fill_gradient2(midpoint = lig_mean
|
||||
|
|
@ -445,7 +446,7 @@ wideP_consurf <- function(plotdf
|
|||
# out = g1
|
||||
# }
|
||||
#
|
||||
############################################################################################
|
||||
############################################################################################
|
||||
#==============================================
|
||||
# x-axis: geom_tiles ~ active sites and others
|
||||
#==============================================
|
||||
|
|
@ -454,48 +455,53 @@ wideP_consurf <- function(plotdf
|
|||
#tW = 1
|
||||
#tH = 0.2
|
||||
|
||||
#---------------------
|
||||
# Add2plot: 3 ligands
|
||||
#---------------------
|
||||
if (all(!is.null(active_aa_pos) &&
|
||||
!is.null(aa_pos_drug) &&
|
||||
!is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && !is.null(aa_pos_lig3))) {
|
||||
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2&3 sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname3)
|
||||
#---------------------
|
||||
# Add2plot: 3 ligands
|
||||
#---------------------
|
||||
if (all(!is.null(active_aa_pos) &&
|
||||
!is.null(aa_pos_drug) &&
|
||||
!is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && !is.null(aa_pos_lig3))) {
|
||||
if (debug){
|
||||
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2&3 sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname3)
|
||||
|
||||
cat("\nDoing Plot with 3 ligands")
|
||||
out = out + geom_tile(aes(,tpos3
|
||||
, width = tW
|
||||
, height = tH )
|
||||
, fill = plotdf[[aa_colour_colname3]]
|
||||
, colour = plotdf[[aa_colour_colname3]]
|
||||
, linetype = "solid") +
|
||||
geom_tile(aes(, tpos2
|
||||
, width = tW
|
||||
, height = tH )
|
||||
, fill = plotdf[[aa_colour_colname2]]
|
||||
, colour = plotdf[[aa_colour_colname2]]
|
||||
, linetype = "solid")+
|
||||
cat("\nDoing Plot with 3 ligands")
|
||||
}
|
||||
out = out + geom_tile(aes(,tpos3
|
||||
, width = tW
|
||||
, height = tH )
|
||||
, fill = plotdf[[aa_colour_colname3]]
|
||||
, colour = plotdf[[aa_colour_colname3]]
|
||||
, linetype = "solid") +
|
||||
geom_tile(aes(, tpos2
|
||||
, width = tW
|
||||
, height = tH )
|
||||
, fill = plotdf[[aa_colour_colname2]]
|
||||
, colour = plotdf[[aa_colour_colname2]]
|
||||
, linetype = "solid")+
|
||||
|
||||
geom_tile(aes(, tpos1
|
||||
, width = tW
|
||||
, height = tH)
|
||||
, fill = plotdf[[aa_colour_colname1]]
|
||||
, colour = plotdf[[aa_colour_colname1]]
|
||||
, linetype = "solid")
|
||||
|
||||
cat("\nDone Plot with 3 ligands")
|
||||
}
|
||||
geom_tile(aes(, tpos1
|
||||
, width = tW
|
||||
, height = tH)
|
||||
, fill = plotdf[[aa_colour_colname1]]
|
||||
, colour = plotdf[[aa_colour_colname1]]
|
||||
, linetype = "solid")
|
||||
if (debug){
|
||||
cat("\nDone Plot with 3 ligands")
|
||||
}
|
||||
}
|
||||
#---------------------
|
||||
# Add2plot: 2 ligands
|
||||
#---------------------
|
||||
if (all(!is.null(active_aa_pos) &&
|
||||
!is.null(aa_pos_drug) &&
|
||||
!is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) {
|
||||
if (debug){
|
||||
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2 sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname2)
|
||||
|
||||
cat("\nDoing Plot with 2 ligands")
|
||||
}
|
||||
out = out +
|
||||
geom_tile(aes(, tpos2
|
||||
, width = tW
|
||||
|
|
@ -509,8 +515,9 @@ wideP_consurf <- function(plotdf
|
|||
, fill = plotdf[[aa_colour_colname1]]
|
||||
, colour = plotdf[[aa_colour_colname1]]
|
||||
, linetype = "solid")
|
||||
|
||||
if (debug){
|
||||
cat("\nDone Plot with 2 ligands")
|
||||
}
|
||||
}
|
||||
|
||||
#---------------------
|
||||
|
|
@ -519,11 +526,12 @@ wideP_consurf <- function(plotdf
|
|||
if (all(!is.null(active_aa_pos) &&
|
||||
!is.null(aa_pos_drug) &&
|
||||
!is.null(aa_pos_lig1) && is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) {
|
||||
if (debug){
|
||||
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1 sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname1)
|
||||
|
||||
cat("\nDoing Plot with 1 ligands")
|
||||
|
||||
}
|
||||
out = out +
|
||||
geom_tile(aes(, tpos1
|
||||
, width = tW
|
||||
|
|
@ -546,20 +554,20 @@ wideP_consurf <- function(plotdf
|
|||
is.null(aa_pos_lig1) &&
|
||||
is.null(aa_pos_lig2) &&
|
||||
is.null(aa_pos_lig3))) {
|
||||
|
||||
if (debug){
|
||||
cat("\n\nAnnotating xvar with active and drug binding sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname)
|
||||
cat("\nDoing Plot with 0 ligands: active and drug site only")
|
||||
|
||||
}
|
||||
out = out + geom_tile(aes(, tpos3
|
||||
, width = tW
|
||||
, height = tH)
|
||||
, fill = plotdf[[aa_colour_colname]]
|
||||
, colour = plotdf[[aa_colour_colname]]
|
||||
, linetype = "solid")
|
||||
|
||||
, width = tW
|
||||
, height = tH)
|
||||
, fill = plotdf[[aa_colour_colname]]
|
||||
, colour = plotdf[[aa_colour_colname]]
|
||||
, linetype = "solid")
|
||||
if (debug){
|
||||
cat("\nDone Plot with: Active and Drug sites")
|
||||
|
||||
}
|
||||
}
|
||||
}else{
|
||||
cat("\nNo annotation for additional ligands on xvar requested")
|
||||
|
|
@ -567,23 +575,23 @@ wideP_consurf <- function(plotdf
|
|||
#==============================================
|
||||
if (A_xvar_lig){
|
||||
legs = cowplot::plot_grid(legend1
|
||||
, legend2
|
||||
, ncol = 1
|
||||
, align = "hv"
|
||||
, rel_heights = c(2/4,3/4))
|
||||
, legend2
|
||||
, ncol = 1
|
||||
, align = "hv"
|
||||
, rel_heights = c(2/4,3/4))
|
||||
|
||||
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
|
||||
, legs
|
||||
, ncol = 2
|
||||
, align = "hv"
|
||||
, rel_widths = c(9/10, 0.4/10)
|
||||
, legs
|
||||
, ncol = 2
|
||||
, align = "hv"
|
||||
, rel_widths = c(9/10, 0.4/10)
|
||||
)
|
||||
}else{
|
||||
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
|
||||
, legend1
|
||||
, ncol = 2
|
||||
, align = "hv"
|
||||
, rel_widths = c(9/10, 0.5/10)
|
||||
, legend1
|
||||
, ncol = 2
|
||||
, align = "hv"
|
||||
, rel_widths = c(9/10, 0.5/10)
|
||||
)
|
||||
}
|
||||
#==============================================
|
||||
|
|
@ -609,8 +617,8 @@ wideP_consurf <- function(plotdf
|
|||
# )
|
||||
# }
|
||||
#==============================================
|
||||
return(out2)
|
||||
#return(out2)
|
||||
return(out2)
|
||||
#return(out2)
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -117,14 +117,16 @@ LogoPlotSnps <- function(plot_df
|
|||
|
||||
if (is.matrix(tab_mt)){
|
||||
cat("\nPASS: Mutant matrix successfully created..."
|
||||
, "\nRownames of mutant matrix:", rownames(tab_mt)
|
||||
, "\nColnames of mutant matrix:", colnames(tab_mt))
|
||||
#, "\nRownames of mutant matrix:", rownames(tab_mt)
|
||||
#, "\nColnames of mutant matrix:", colnames(tab_mt)
|
||||
)
|
||||
} else{
|
||||
tab_mt = as.matrix(tab_mt, rownames = T)
|
||||
if (is.matrix(tab_mt)){
|
||||
cat("\nCreating mutant matrix..."
|
||||
, "\nRownames of mutant matrix:", rownames(tab_mt)
|
||||
, "\nColnames of mutant matrix:", colnames(tab_mt))
|
||||
#, "\nRownames of mutant matrix:", rownames(tab_mt)
|
||||
#, "\nColnames of mutant matrix:", colnames(tab_mt)
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -151,8 +153,9 @@ LogoPlotSnps <- function(plot_df
|
|||
, "\nDim of wt matrix:", dim(tab_wt)
|
||||
, "\nDim of mutant matrix:", dim(tab_mt)
|
||||
, "\n"
|
||||
, "\nRownames of mutant matrix:", rownames(tab_wt)
|
||||
, "\nColnames of mutant matrix:", colnames(tab_wt))
|
||||
#, "\nRownames of mutant matrix:", rownames(tab_wt)
|
||||
#, "\nColnames of mutant matrix:", colnames(tab_wt)
|
||||
)
|
||||
}
|
||||
|
||||
######################################
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue