tests/geom_linelabel_test.R
In alexcoulton/gglinelabel: What the Package Does (One Line, Title Case)
source('~/work/ucl/scripts/misc/functions.R')
library(devtools)
library(ggplot2)
library(dplyr)
library(ggplot2testing)
library(gglinelabel)
library(ggrepel)
library(rmarkdown)
#render('./vignettes/using-gglinelabel.Rmd')
load_all('~/work/external.repos/gglinelabel/')
data(chr1)
#chr1 = get.genes(1, 0, 1000000000000)
#chr1$expression = rnorm(nrow(chr1))
#chr1$expression[chr1$expression < 0] = 0
#chr1 = chr1[c('chr', 'start', 'end', 'gene', 'expression')]
#chr1$sig.genes = NA
#chr1$sig.genes[chr1$expression > 0.7] = chr1$gene[chr1$expression > 0.7]
#chr1$cosmic = NA
#chr1$cosmic[is.cosmic(chr1$gene) & chr1$expression > 1.5] = chr1$gene[is.cosmic(chr1$gene) & chr1$expression > 1.5]
#chr1$cosmic[which(chr1$cosmic == 'AKT3') + 1] = 'TEST'
#saveRDS(chr1, '~/work/external.repos/gglinelabel/tests/chr1.ggrepel.fail.rds')
#chr1 = readRDS('~/work/external.repos/gglinelabel/tests/chr1.ggrepel.fail.rds')
#save(chr1, file = '~/work/external.repos/gglinelabel/data/chr1orderggrepel.rda')
#data(chr1orderggrepel)
plot1 = ggplot(chr1, aes(x = start, y = expression, label = cosmic)) +
geom_bar(stat = 'identity') +
#geom_line() +
#geom_linelabel(
#layout = 'fan',
#text.size = 4
#) +
geom_text_repel(
nudge_y = 10,
direction = 'x',
angle = 90,
force = 10,
nudge_x = c(0, 0, 10, 1000000000)
) +
coord_cartesian(ylim = c(0, 4))
#pl(plot1, 15, 5)
head(chr1)
plot1 = ggplot(chr1, aes(x = start, y = expression, label = gene)) +
geom_line(stat = 'identity') +
#geom_line() +
geom_linelabel(
layout = 'cloud',
text.size = 3,
fan.height = 10
#spread.factor = 0
) +
coord_cartesian(ylim = c(0, 300))
pl(plot1, 15, 5)
devtools::test()
load_all('~/work/external.repos/gglinelabel/')
plot1 = ggplot(chr1, aes(x = start, y = expression, label = gene)) +
geom_line(stat = 'identity') +
#geom_line() +
geom_linelabel(
layout = 'fan',
text.size = 3,
min.y = 170,
max.y = 200,
fan.height = 0.4
#spread.factor = 1,
#spread.threshold = 100000000000
) +
coord_cartesian(ylim = c(0, 300))
pl(plot1, 15, 5)
plot1 = ggplot(chr1, aes(x = start, y = expression, label = cosmic)) +
geom_bar(stat = 'identity') +
#geom_line() +
geom_linelabel(
layout = 'straight',
spread.factor = 0.04,
spread.threshold = 10000000,
max.y = 3
)
#pl(plot1, 15, 5)
plot1 = ggplot(chr1, aes(x = start, y = expression, label = cosmic)) +
geom_bar(stat = 'identity') +
#geom_line() +
geom_linelabel(
fan.height = 0.7,
spread.factor = 0.2,
spread.threshold = 1000000
)
#pl(plot1, 15, 5)
plot.ggrepel = ggplot(chr1, aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_text_repel(
nudge_y = 250,
direction = 'x',
hjust = 0,
angle = 90,
segment.color = "grey50",
segment.linetype = 'dotted'
) +
scale_y_continuous(limits = c(NA, 5))
#pl(plot.ggrepel, 5, 5)
#pl(plot1)
#save(chr1, file = '~/work/external.repos/gglinelabel/data/chr1.rda')
data(chr1)
chr1$gene[[2]] = chr1$gene[[1]]
chr1$gene[30:40] = chr1$gene[[1]]
#pl(plot1)
chr1 = chr1[1:30, ]
#devtools::install('~/work/external.repos/ggplot2_testing/')
#source('~/work/external.repos/ggplot2_testing/R/geom-point.r')
#source('~/work/external.repos/ggplot2_testing/R/layer.r')
label.df = chr1[c('gene', 'expression')]
test_function = function(){
layer_data(data)
}
linelabel_chr = chr1[c('start', 'expression', 'gene')]
colnames(linelabel_chr) = c('x', 'y', 'label')
topnum = 30
chr1.new = chr1
#chr1.new[sample(1:100, 70), ]$gene = NA
expression.gen = rnorm(100)
expression.gen[expression.gen < 0] = 0
expression.gen = expression.gen * 100
chr1.new$expression = expression.gen[1:nrow(chr1.new)]
chr1.new$sig.genes = NA
chr1.new$sig.genes[chr1.new$expression > 100] = chr1.new$gene[chr1.new$expression > 100]
plot.ggrepel = ggplot(chr1.new[1:topnum, ], aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_text_repel(
nudge_y = 250,
direction = 'x',
hjust = 1,
angle = 90,
segment.color = "grey50",
segment.linetype = 'dotted'
) +
scale_y_continuous(limits = c(NA, 330))
#geom_simple_point(angle = 90, hjust = 0, text.size = 2, layout = 'star', linetype = 'dotted') +
#geom_simple_point(colour = '#d8d654', linetype = 'dashed') +
#pl(
ggplot(chr1.new, aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_text_repel(
nudge_y = 250,
direction = 'x',
hjust = 1,
angle = 90,
segment.color = "grey50",
segment.linetype = 'dotted'
) +
scale_y_continuous(limits = c(NA, 330))
)
chr1.new
#pl(
#ggplot(chr1.new, aes(x = start, y = expression, label = sig.genes)) +
#geom_point() +
#geom_line() +
##geom_linelabel() +
#scale_y_continuous(limits = c(NA, 330))
#)
#pl(plot.ggrepel, 5, 5)
topnum = 30
plot.star = ggplot(chr1.new[1:topnum, ], aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_linelabel(layout = 'fan', nudge_y = 0, spread.iter = 1000) +
scale_y_continuous(limits = c(NA, 5)) +
coord_cartesian(ylim = c(0, 400))
pl(plot.star, 5, 5)
plot.straight = ggplot(chr1.new[1:topnum, ], aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_linelabel(layout = 'straight', nudge_y = -20) +
scale_y_continuous(limits = c(NA, 300)) +
coord_cartesian(ylim = c(0, 800))
#pl(plot.straight)
plot.cloud = ggplot(chr1.new[1:topnum, ], aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_linelabel(layout = 'cloud', nudge_y = -20, text.size = 4) +
coord_cartesian(ylim = c(0, 400))
#pl(plot.cloud)
chr1$gene[chr1$expression < 1] = NA
chr1$nudge = 0
chr1$nudge[chr1$gene == 'LINC01128'] = 20000
plot.fan = ggplot(chr1, aes(x = start, y = expression, label = gene)) +
geom_point() +
geom_line() +
geom_linelabel(layout = 'straight', nudge_y = -0, text.size = 2, aes(nudge_label = nudge, max.y = 2.3)) +
coord_cartesian(ylim = c(0, 3))
#pl(plot.fan, 10, 10)
cn.dat = data.frame(
sample = 'test',
chr = 1,
start = c(1, 40001, 100001, 106101),
end = c(40000, 100000, 106100, 200000),
cn = c(2, 1, 3, 2)
)
cn.dat + geom_linelabel(aes(label = sample))
make.copy.number.plot
make.copy.number.plot = function(
cn.df,
ylim1 = c(0, 10),
ybreaks = seq(0, 10, 2),
colnames1 = c('sample', 'chr', 'start', 'end', 'cn'),
yintercept1 = 2
){
library(gdata)
#args:
#cn.df: data.frame with columns sample, chr, start, end, cn and patient
cn.df.p1 = cn.df[c('sample', 'chr', 'start', 'cn')]
colnames(cn.df.p1)[3] = 'point'
cn.df.p2 = cn.df[c('sample', 'chr', 'end', 'cn')]
colnames(cn.df.p2)[3] = 'point'
cn.df = interleave(cn.df.p1, cn.df.p2)
ggplot(cn.df, aes(x = point, y = cn)) +
coord_cartesian(ylim = ylim1) +
geom_hline(yintercept = yintercept1, color = 'red', linetype = 'dotted') +
scale_y_continuous(breaks = ybreaks) +
facet_grid(cols = vars(chr), scales = 'free_x') +
geom_line() +
rot.lab() +
xlab('Position')
}
chr.test = chr1.new[1:30, ]
chr.test = chr.test[1:6, ]
chr.test = chr.test[c('chr', 'start', 'end', 'gene', 'expression')]
cn.ranges = GRanges(cn.dat)
chr.ranges = GRanges(chr.test)
overlaps = as.data.frame(findOverlaps(cn.ranges, chr.ranges))
chr.test = chr.test[overlaps$subjectHits, ]
chr.test$cn = cn.dat[overlaps$queryHits, ]$cn
nudge_label = 100000
names(nudge_label) = 'OR4F5'
chr.test$nudge = 0
chr.test$nudge[chr.test$gene == 'OR4F5'] = 100000
nudgelayout = 'straight'
newplot = make.copy.number.plot(cn.dat) +
geom_linelabel(
data = chr.test,
inherit.aes = F,
aes(
x = start,
y = cn,
label = gene,
layout = nudgelayout,
nudge_label = nudge
),
spread.iter = 100,
nudge_y = -5,
#cloud.straight = T,
#label.straight = T,
#min.y = 4,
fan.height = -2,
#angle = 0,
#angle = 270,
min.x = 1,
max.x = 200000,
#min.y = -4,
#max.y = -7,
rotate = 0,
color = 'red',
text.colour = 'blue'
#linetype = 'solid'
) +
geom_point() +
coord_cartesian(ylim = c(-10, 10))
#pl(newplot)
newplot = make.copy.number.plot(cn.dat) +
geom_linelabel(
data = chr.test,
inherit.aes = F,
aes(
x = start,
y = cn,
label = gene,
layout = nudgelayout
),
spread.iter = 100,
nudge_y = -5,
#cloud.straight = T,
#label.straight = T,
#min.y = 4,
fan.height = -2,
#angle = 0,
#angle = 270,
min.x = 1,
max.x = 200000,
#min.y = -4,
#max.y = -7,
rotate = 0,
color = 'red',
text.colour = 'blue'
#linetype = 'solid'
) +
geom_point() +
coord_cartesian(ylim = c(-10, 10))
#pl(newplot)
library(reshape2)
cn.dat$group = 1:nrow(cn.dat)
cn.dat
cn.dat2 = melt(cn.dat, id = c('cn', 'group'))
#pl(ggplot(cn.dat2, aes(x = value, y = cn, group = group)) + geom_line())
alexcoulton/gglinelabel documentation built on June 23, 2022, 4:49 a.m.
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source('~/work/ucl/scripts/misc/functions.R')
library(devtools)
library(ggplot2)
library(dplyr)
library(ggplot2testing)
library(gglinelabel)
library(ggrepel)
library(rmarkdown)
#render('./vignettes/using-gglinelabel.Rmd')
load_all('~/work/external.repos/gglinelabel/')
data(chr1)
#chr1 = get.genes(1, 0, 1000000000000)
#chr1$expression = rnorm(nrow(chr1))
#chr1$expression[chr1$expression < 0] = 0
#chr1 = chr1[c('chr', 'start', 'end', 'gene', 'expression')]
#chr1$sig.genes = NA
#chr1$sig.genes[chr1$expression > 0.7] = chr1$gene[chr1$expression > 0.7]
#chr1$cosmic = NA
#chr1$cosmic[is.cosmic(chr1$gene) & chr1$expression > 1.5] = chr1$gene[is.cosmic(chr1$gene) & chr1$expression > 1.5]
#chr1$cosmic[which(chr1$cosmic == 'AKT3') + 1] = 'TEST'
#saveRDS(chr1, '~/work/external.repos/gglinelabel/tests/chr1.ggrepel.fail.rds')
#chr1 = readRDS('~/work/external.repos/gglinelabel/tests/chr1.ggrepel.fail.rds')
#save(chr1, file = '~/work/external.repos/gglinelabel/data/chr1orderggrepel.rda')
#data(chr1orderggrepel)
plot1 = ggplot(chr1, aes(x = start, y = expression, label = cosmic)) +
geom_bar(stat = 'identity') +
#geom_line() +
#geom_linelabel(
#layout = 'fan',
#text.size = 4
#) +
geom_text_repel(
nudge_y = 10,
direction = 'x',
angle = 90,
force = 10,
nudge_x = c(0, 0, 10, 1000000000)
) +
coord_cartesian(ylim = c(0, 4))
#pl(plot1, 15, 5)
head(chr1)
plot1 = ggplot(chr1, aes(x = start, y = expression, label = gene)) +
geom_line(stat = 'identity') +
#geom_line() +
geom_linelabel(
layout = 'cloud',
text.size = 3,
fan.height = 10
#spread.factor = 0
) +
coord_cartesian(ylim = c(0, 300))
pl(plot1, 15, 5)
devtools::test()
load_all('~/work/external.repos/gglinelabel/')
plot1 = ggplot(chr1, aes(x = start, y = expression, label = gene)) +
geom_line(stat = 'identity') +
#geom_line() +
geom_linelabel(
layout = 'fan',
text.size = 3,
min.y = 170,
max.y = 200,
fan.height = 0.4
#spread.factor = 1,
#spread.threshold = 100000000000
) +
coord_cartesian(ylim = c(0, 300))
pl(plot1, 15, 5)
plot1 = ggplot(chr1, aes(x = start, y = expression, label = cosmic)) +
geom_bar(stat = 'identity') +
#geom_line() +
geom_linelabel(
layout = 'straight',
spread.factor = 0.04,
spread.threshold = 10000000,
max.y = 3
)
#pl(plot1, 15, 5)
plot1 = ggplot(chr1, aes(x = start, y = expression, label = cosmic)) +
geom_bar(stat = 'identity') +
#geom_line() +
geom_linelabel(
fan.height = 0.7,
spread.factor = 0.2,
spread.threshold = 1000000
)
#pl(plot1, 15, 5)
plot.ggrepel = ggplot(chr1, aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_text_repel(
nudge_y = 250,
direction = 'x',
hjust = 0,
angle = 90,
segment.color = "grey50",
segment.linetype = 'dotted'
) +
scale_y_continuous(limits = c(NA, 5))
#pl(plot.ggrepel, 5, 5)
#pl(plot1)
#save(chr1, file = '~/work/external.repos/gglinelabel/data/chr1.rda')
data(chr1)
chr1$gene[[2]] = chr1$gene[[1]]
chr1$gene[30:40] = chr1$gene[[1]]
#pl(plot1)
chr1 = chr1[1:30, ]
#devtools::install('~/work/external.repos/ggplot2_testing/')
#source('~/work/external.repos/ggplot2_testing/R/geom-point.r')
#source('~/work/external.repos/ggplot2_testing/R/layer.r')
label.df = chr1[c('gene', 'expression')]
test_function = function(){
layer_data(data)
}
linelabel_chr = chr1[c('start', 'expression', 'gene')]
colnames(linelabel_chr) = c('x', 'y', 'label')
topnum = 30
chr1.new = chr1
#chr1.new[sample(1:100, 70), ]$gene = NA
expression.gen = rnorm(100)
expression.gen[expression.gen < 0] = 0
expression.gen = expression.gen * 100
chr1.new$expression = expression.gen[1:nrow(chr1.new)]
chr1.new$sig.genes = NA
chr1.new$sig.genes[chr1.new$expression > 100] = chr1.new$gene[chr1.new$expression > 100]
plot.ggrepel = ggplot(chr1.new[1:topnum, ], aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_text_repel(
nudge_y = 250,
direction = 'x',
hjust = 1,
angle = 90,
segment.color = "grey50",
segment.linetype = 'dotted'
) +
scale_y_continuous(limits = c(NA, 330))
#geom_simple_point(angle = 90, hjust = 0, text.size = 2, layout = 'star', linetype = 'dotted') +
#geom_simple_point(colour = '#d8d654', linetype = 'dashed') +
#pl(
ggplot(chr1.new, aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_text_repel(
nudge_y = 250,
direction = 'x',
hjust = 1,
angle = 90,
segment.color = "grey50",
segment.linetype = 'dotted'
) +
scale_y_continuous(limits = c(NA, 330))
)
chr1.new
#pl(
#ggplot(chr1.new, aes(x = start, y = expression, label = sig.genes)) +
#geom_point() +
#geom_line() +
##geom_linelabel() +
#scale_y_continuous(limits = c(NA, 330))
#)
#pl(plot.ggrepel, 5, 5)
topnum = 30
plot.star = ggplot(chr1.new[1:topnum, ], aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_linelabel(layout = 'fan', nudge_y = 0, spread.iter = 1000) +
scale_y_continuous(limits = c(NA, 5)) +
coord_cartesian(ylim = c(0, 400))
pl(plot.star, 5, 5)
plot.straight = ggplot(chr1.new[1:topnum, ], aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_linelabel(layout = 'straight', nudge_y = -20) +
scale_y_continuous(limits = c(NA, 300)) +
coord_cartesian(ylim = c(0, 800))
#pl(plot.straight)
plot.cloud = ggplot(chr1.new[1:topnum, ], aes(x = start, y = expression, label = sig.genes)) +
geom_point() +
geom_line() +
geom_linelabel(layout = 'cloud', nudge_y = -20, text.size = 4) +
coord_cartesian(ylim = c(0, 400))
#pl(plot.cloud)
chr1$gene[chr1$expression < 1] = NA
chr1$nudge = 0
chr1$nudge[chr1$gene == 'LINC01128'] = 20000
plot.fan = ggplot(chr1, aes(x = start, y = expression, label = gene)) +
geom_point() +
geom_line() +
geom_linelabel(layout = 'straight', nudge_y = -0, text.size = 2, aes(nudge_label = nudge, max.y = 2.3)) +
coord_cartesian(ylim = c(0, 3))
#pl(plot.fan, 10, 10)
cn.dat = data.frame(
sample = 'test',
chr = 1,
start = c(1, 40001, 100001, 106101),
end = c(40000, 100000, 106100, 200000),
cn = c(2, 1, 3, 2)
)
cn.dat + geom_linelabel(aes(label = sample))
make.copy.number.plot
make.copy.number.plot = function(
cn.df,
ylim1 = c(0, 10),
ybreaks = seq(0, 10, 2),
colnames1 = c('sample', 'chr', 'start', 'end', 'cn'),
yintercept1 = 2
){
library(gdata)
#args:
#cn.df: data.frame with columns sample, chr, start, end, cn and patient
cn.df.p1 = cn.df[c('sample', 'chr', 'start', 'cn')]
colnames(cn.df.p1)[3] = 'point'
cn.df.p2 = cn.df[c('sample', 'chr', 'end', 'cn')]
colnames(cn.df.p2)[3] = 'point'
cn.df = interleave(cn.df.p1, cn.df.p2)
ggplot(cn.df, aes(x = point, y = cn)) +
coord_cartesian(ylim = ylim1) +
geom_hline(yintercept = yintercept1, color = 'red', linetype = 'dotted') +
scale_y_continuous(breaks = ybreaks) +
facet_grid(cols = vars(chr), scales = 'free_x') +
geom_line() +
rot.lab() +
xlab('Position')
}
chr.test = chr1.new[1:30, ]
chr.test = chr.test[1:6, ]
chr.test = chr.test[c('chr', 'start', 'end', 'gene', 'expression')]
cn.ranges = GRanges(cn.dat)
chr.ranges = GRanges(chr.test)
overlaps = as.data.frame(findOverlaps(cn.ranges, chr.ranges))
chr.test = chr.test[overlaps$subjectHits, ]
chr.test$cn = cn.dat[overlaps$queryHits, ]$cn
nudge_label = 100000
names(nudge_label) = 'OR4F5'
chr.test$nudge = 0
chr.test$nudge[chr.test$gene == 'OR4F5'] = 100000
nudgelayout = 'straight'
newplot = make.copy.number.plot(cn.dat) +
geom_linelabel(
data = chr.test,
inherit.aes = F,
aes(
x = start,
y = cn,
label = gene,
layout = nudgelayout,
nudge_label = nudge
),
spread.iter = 100,
nudge_y = -5,
#cloud.straight = T,
#label.straight = T,
#min.y = 4,
fan.height = -2,
#angle = 0,
#angle = 270,
min.x = 1,
max.x = 200000,
#min.y = -4,
#max.y = -7,
rotate = 0,
color = 'red',
text.colour = 'blue'
#linetype = 'solid'
) +
geom_point() +
coord_cartesian(ylim = c(-10, 10))
#pl(newplot)
newplot = make.copy.number.plot(cn.dat) +
geom_linelabel(
data = chr.test,
inherit.aes = F,
aes(
x = start,
y = cn,
label = gene,
layout = nudgelayout
),
spread.iter = 100,
nudge_y = -5,
#cloud.straight = T,
#label.straight = T,
#min.y = 4,
fan.height = -2,
#angle = 0,
#angle = 270,
min.x = 1,
max.x = 200000,
#min.y = -4,
#max.y = -7,
rotate = 0,
color = 'red',
text.colour = 'blue'
#linetype = 'solid'
) +
geom_point() +
coord_cartesian(ylim = c(-10, 10))
#pl(newplot)
library(reshape2)
cn.dat$group = 1:nrow(cn.dat)
cn.dat
cn.dat2 = melt(cn.dat, id = c('cn', 'group'))
#pl(ggplot(cn.dat2, aes(x = value, y = cn, group = group)) + geom_line())
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