Create barplot "sample.order" option doesn't work properly when stack = TRUE #48
Description
I believe this has been an issue for a long time unless I miss something but the sample.order ("increasing/decreasing") option in create.barplot doesn't work properly when stack = TRUE. BoutrosLab.plotting.general_7.0.3 was used to generate the plots below.
Without sample.order
create.barplot(
filename = "stack.png",
formula = values ~ samples,
data = barplot.data,
main = 'Stacked bar chart',
xlab.lab = 'Samples',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
groups = mutation,
col = default.colours(12, is.greyscale = FALSE)[11:12],
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 2,
# reverse order to match stacked bar order
fill = rev(default.colours(12, is.greyscale = FALSE)[11:12])
),
text = list(
# reverse order to match stacked bar order
lab = rev(c('Nonsynonymous SNV','Other SNV'))
),
padding.text = 3,
cex = 1
)
),
x = 0.55,
y = 0.95
)
),
# Changing the plot from a grouped plot to a stacked plot
stack = TRUE,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
sample.order = 'decreasing'
create.barplot(
filename = "stack_decreasing.png",
formula = values ~ samples,
data = barplot.data,
main = 'Stacked bar chart',
xlab.lab = 'Samples',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
groups = mutation,
col = default.colours(12, is.greyscale = FALSE)[11:12],
sample.order = 'decreasing',
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 2,
# reverse order to match stacked bar order
fill = rev(default.colours(12, is.greyscale = FALSE)[11:12])
),
text = list(
# reverse order to match stacked bar order
lab = rev(c('Nonsynonymous SNV','Other SNV'))
),
padding.text = 3,
cex = 1
)
),
x = 0.55,
y = 0.95
)
),
# Changing the plot from a grouped plot to a stacked plot
stack = TRUE,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
sample.order = 'increasing'
create.barplot(
filename = "stack_increasing.png",
formula = values ~ samples,
data = barplot.data,
main = 'Stacked bar chart',
xlab.lab = 'Samples',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
groups = mutation,
col = default.colours(12, is.greyscale = FALSE)[11:12],
sample.order = 'increasing',
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 2,
# reverse order to match stacked bar order
fill = rev(default.colours(12, is.greyscale = FALSE)[11:12])
),
text = list(
# reverse order to match stacked bar order
lab = rev(c('Nonsynonymous SNV','Other SNV'))
),
padding.text = 3,
cex = 1
)
),
x = 0.55,
y = 0.95
)
),
# Changing the plot from a grouped plot to a stacked plot
stack = TRUE,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
