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Merge branch 'master' of https://git.tunstall.in/tanu/LSHTM_analysis

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This commit is contained in:
Tanushree Tunstall 2022-05-05 13:36:03 +01:00
commit d61d11e020
6 changed files with 33 additions and 14 deletions
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2
scripts/functions/bp_lineage.R
View file

@ -5,9 +5,9 @@
########################################
lin_count_bp <- function( lf_data = lin_lf
, all_lineages = F
, x_categ = "sel_lineages"
, y_count = "p_count"
, all_lineages = F
, use_lineages = c("L1", "L2", "L3", "L4")
, bar_fill_categ = "count_categ"
, display_label_col = "p_count"

33
scripts/functions/consurfP.R
View file

@ -238,12 +238,31 @@ wideP_consurf <- function(plotdf
my_xlim = length(unique(plotdf[[xvar_colname]])); my_xlim
ymin = min(plotdf[[yvar_colname]]); ymin
ymax = max(plotdf[[yvar_colname]]); ymax
# DEBUG
# x_factor = as.factor(plotdf[[xvar_colname]])
# y_colour_factor = as.factor(plotdf[[yvar_colourN_colname]])
# cat('XXXX THIS:', str(x_factor))
#
# g = ggplot(plotdf, aes_string(x = x_factor)
# , y = yvar_colname
# , 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)
))
# "if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
))
# g = ggplot(plotdf, aes_string(x = "position")
# , y = "consurf_score"
# , colour = "consurf_colour_rev")
# g = ggplot(plotdf, aes_string(x = "position")
# , y = "consurf_score"
# , colour = "consurf_colour_rev")
# DEBUG
#g0=g
"if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
if (plot_type == "bar"){
g0 = g +
geom_bar(stat = "identity")
@ -260,15 +279,15 @@ wideP_consurf <- function(plotdf
}
if (plot_error_bars){
g0 = g0 +
g0 = g0 +
geom_errorbar(aes(ymin = eval(parse(text = lower_EB_colname))
, ymax = eval(parse(text = upper_EB_colname))
))
}else{
g0 = g0
}
g0 = g0
}
#---------------------
# add axis formatting

2
scripts/functions/lf_bp.R
View file

@ -8,7 +8,7 @@
lf_bp <- function(lf_df = lf_duet
, p_title = "DUET-DDG"
, colour_categ = "duet_outcome"
, colour_categ = "outcome"
, x_grp = "mutation_info_labels"
, y_var = "param_value"
, facet_var = "param_type"

4
scripts/functions/logoP_snp.R
View file

@ -52,8 +52,8 @@ LogoPlotSnps <- function(plot_df
{
# handle funky omit_snp_count. DOES NOT WORK YET
if (class(omit_snp_count != 'numeric')){
omit_snp_count <- as.numeric(unlist(str_extract_all(thing, regex("[0-9]"))))
if (class(omit_snp_count) != "numeric"){
omit_snp_count <- as.numeric(unlist(str_extract_all(omit_snp_count, regex("[0-9]+"))))
}
############################################
# Data processing for logo plot for nsSNPS

2
scripts/functions/my_pairs_panel.R
View file

@ -40,7 +40,7 @@ my_corr_pairs <- function (corr_data_all
######################################################################
my_pp = function (x, smooth = TRUE, scale = FALSE, density = TRUE, ellipses = TRUE,
digits = 2, method = "pearson", pch = 20, lm = FALSE, cor = TRUE,
digits = 2, method = "spearman", pch = 20, lm = FALSE, cor = TRUE,
jiggle = FALSE, factor = 2, hist.col = "cyan", show.points = TRUE,
rug = TRUE, breaks = "Sturges", cex.cor = 1, wt = NULL, smoother = FALSE,
stars = FALSE, ci = FALSE, alpha = 0.05, ...)

4
scripts/functions/stability_count_bp.R
View file

@ -15,8 +15,8 @@ theme_set(theme_grey())
## ...opt args
#==========================================================
stability_count_bp <- function(plotdf
, df_colname = "duet_outcome"
, leg_title = "DUET"
, df_colname = ""
, leg_title = ""
, ats = 25 # axis text size
, als = 22 # axis label size
, lts = 20 # legend text size