about ECDF display in ggplot2

Discussion:

Bogdan Tanasa

2018-07-06 23:37:37 UTC

Dear all,

I would appreciate having your advice/suggestions/comments on the following
:

1 -- starting from a vector that contains LENGTHS (numerically, the values
are from 1 to 10 000)

2 -- shall I display the ECDF by using the R code and some "limits" :

BREAKS = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500,
1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000)

ggplot(x, aes(LENGTH)) +
stat_ecdf(geom = "point") +
scale_x_continuous(name = "LENGTH of DEL",
breaks = BREAKS,
limits=c(0, 500))

3 -- I am getting the following warning message : "Warning message: Removed
109 rows containing non-finite values (stat_ecdf)."

The question is : are these 109 values removed from VISUALIZATION as i set
up the "limits", or are these 109 values removed from statistical
CALCULATION?

4 -- in contrast, shall I use the standard R functions plot(ecdf), there is
no "warning mesage"

plot(ecdf(x$LENGTH), xlab="DEL LENGTH",
ylab="Fraction of DEL", main="DEL", xlim=c(0,500),
col = "dark red")

Thanks a lot !

-- bogdan
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Edson Lira

2018-07-07 02:20:10 UTC

Permalink

Check yours data: outlyers, format, NA's

Post by Bogdan Tanasa
Dear all,
I would appreciate having your advice/suggestions/comments on the
1 -- starting from a vector that contains LENGTHS (numerically, the values
are from 1 to 10 000)
BREAKS = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500,
1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000)
ggplot(x, aes(LENGTH)) +
stat_ecdf(geom = "point") +
scale_x_continuous(name = "LENGTH of DEL",
breaks = BREAKS,
limits=c(0, 500))
Removed 109 rows containing non-finite values (stat_ecdf)."
The question is : are these 109 values removed from VISUALIZATION as i set
up the "limits", or are these 109 values removed from statistical
CALCULATION?
4 -- in contrast, shall I use the standard R functions plot(ecdf), there
is no "warning mesage"
plot(ecdf(x$LENGTH), xlab="DEL LENGTH",
ylab="Fraction of DEL", main="DEL", xlim=c(0,500),
col = "dark red")
Thanks a lot !
-- bogdan
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https://github.com/hadley/devtools/wiki/Reproducibility
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Bogdan Tanasa

2018-07-09 00:49:27 UTC

Permalink

Dear all,

following up on my previous email regarding ECDF in ggplot2, in order to be
more descriptive/comprehensive, 've attached to my email the following
files (as I do not have a web server running at this moment ... I would
welcome your suggestions on how to post these files online) :

1 -- the R script (R_script_display_ECDF.R) that reads the file "LENGTH"
and outputs ECDF figure by using the standard R function or ggplot2.

2 -- the display of ECDF by using standard R function
("display.R.ecdf.LENGTH.pdf")

3 -- the display of ECDF by using ggplot2 ("display.ggplot2.ecdf.LENGTH.
pdf")

The ECDF over xlim(0,500) looks very different (contrasting plot(ecdf) vs
ggplot2). Please would you advise why ? what shall I change in my ggplot2
code ?

thanks a lot,

- bogdan

ps : the R code is also written below :

library("ggplot2")

file <- read.delim("LENGTH", sep="\t", header=T, stringsAsFactors=F)
pdf("display.R.ecdf.LENGTH.pdf", width=10, height=6, paper='special')
plot(ecdf(file$LENGTH), xlab="DEL SIZE",
ylab="fraction of DEL",
main="LENGTH of DEL",
xlim=c(0,500),
col = "dark red", axes = FALSE)
ticks_y <- c(0, 0.2, 0.4, 0.6, 0.8, 1, 1.2, 1.4)
axis(2, at=ticks_y, labels=ticks_y, col.axis="red")
ticks_x <- c(0, 100, 200, 400, 500, 600, 700, 800)
axis(1, at=ticks_x, labels=ticks_x, col.axis="blue")
dev.off()
BREAKS = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500,
1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000)
barfill <- "#4271AE"
barlines <- "#1F3552"
pdf("display.ggplot2.ecdf.LENGTH.pdf", width=10, height=6,
paper='special')
ggplot(file, aes(LENGTH)) +
stat_ecdf(geom = "point", colour = barlines, fill = barfill) +
scale_x_continuous(name = "LENGTH of DEL",
breaks = BREAKS,
limits=c(0, 500)) +
scale_y_continuous(name = "FRACTION") +
ggtitle("ECDF of LENGTH") +
theme_bw() +
theme(legend.position = "bottom", legend.direction =
"horizontal",
legend.box = "horizontal",
legend.key.size = unit(1, "cm"),
axis.title = element_text(size = 12),
legend.text = element_text(size = 9),
legend.title=element_text(face = "bold", size = 9))
dev.off()
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about ECDF display in ggplot2
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Dear all,
I would appreciate having your advice/suggestions/comments on the following
1 -- starting from a vector that contains LENGTHS (numerically, the values
are from 1 to 10 000)
BREAKS = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500,
1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000)
ggplot(x, aes(LENGTH)) +
stat_ecdf(geom = "point") +
scale_x_continuous(name = "LENGTH of DEL",
breaks = BREAKS,
limits=c(0, 500))
3 -- I am getting the following warning message : "Warning message: Removed
109 rows containing non-finite values (stat_ecdf)."
The question is : are these 109 values removed from VISUALIZATION as i set
up the "limits", or are these 109 values removed from statistical
CALCULATION?
4 -- in contrast, shall I use the standard R functions plot(ecdf), there is
no "warning mesage"
plot(ecdf(x$LENGTH), xlab="DEL LENGTH",
ylab="Fraction of DEL", main="DEL", xlim=c(0,500),
col = "dark red")
Thanks a lot !
-- bogdan
Check yours data: outlyers, format, NA's
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Hadley Wickham

2018-07-09 02:23:51 UTC

Permalink

I would highly recommend that you create a reprex, see
https://www.tidyverse.org/help/ for some details.
Hadley

Post by Bogdan Tanasa
Dear all,
following up on my previous email regarding ECDF in ggplot2, in order to
be more descriptive/comprehensive, 've attached to my email the following
files (as I do not have a web server running at this moment ... I would
1 -- the R script (R_script_display_ECDF.R) that reads the file "LENGTH"
and outputs ECDF figure by using the standard R function or ggplot2.
2 -- the display of ECDF by using standard R function
("display.R.ecdf.LENGTH.pdf")
3 -- the display of ECDF by using ggplot2 ("display.ggplot2.ecdf.LENGTH.
pdf")
The ECDF over xlim(0,500) looks very different (contrasting plot(ecdf) vs
ggplot2). Please would you advise why ? what shall I change in my ggplot2
code ?
thanks a lot,
- bogdan
library("ggplot2")

file <- read.delim("LENGTH", sep="\t", header=T, stringsAsFactors=F)
pdf("display.R.ecdf.LENGTH.pdf", width=10, height=6, paper='special')
plot(ecdf(file$LENGTH), xlab="DEL SIZE",
ylab="fraction of DEL",
main="LENGTH of DEL",
xlim=c(0,500),
col = "dark red", axes = FALSE)
ticks_y <- c(0, 0.2, 0.4, 0.6, 0.8, 1, 1.2, 1.4)
axis(2, at=ticks_y, labels=ticks_y, col.axis="red")
ticks_x <- c(0, 100, 200, 400, 500, 600, 700, 800)
axis(1, at=ticks_x, labels=ticks_x, col.axis="blue")
dev.off()
BREAKS = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500,
1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000)
barfill <- "#4271AE"
barlines <- "#1F3552"
pdf("display.ggplot2.ecdf.LENGTH.pdf", width=10, height=6,
paper='special')
ggplot(file, aes(LENGTH)) +
stat_ecdf(geom = "point", colour = barlines, fill = barfill) +
scale_x_continuous(name = "LENGTH of DEL",
breaks = BREAKS,
limits=c(0, 500)) +
scale_y_continuous(name = "FRACTION") +
ggtitle("ECDF of LENGTH") +
theme_bw() +
theme(legend.position = "bottom", legend.direction =
"horizontal",
legend.box = "horizontal",
legend.key.size = unit(1, "cm"),
axis.title = element_text(size = 12),
legend.text = element_text(size = 9),
legend.title=element_text(face = "bold", size = 9))
dev.off()
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<#m_-280299680146272914_m_-7344921586430841409_group_thread_0> - 2
Updates
about ECDF display in ggplot2
<http://groups.google.com/group/ggplot2/t/a99ce2e3708eee76?utm_source=digest&utm_medium=email>
Dear all,
I would appreciate having your advice/suggestions/comments on the following
1 -- starting from a vector that contains LENGTHS (numerically, the values
are from 1 to 10 000)
BREAKS = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500,
1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000)
ggplot(x, aes(LENGTH)) +
stat_ecdf(geom = "point") +
scale_x_continuous(name = "LENGTH of DEL",
breaks = BREAKS,
limits=c(0, 500))
3 -- I am getting the following warning message : "Warning message: Removed
109 rows containing non-finite values (stat_ecdf)."
The question is : are these 109 values removed from VISUALIZATION as i set
up the "limits", or are these 109 values removed from statistical
CALCULATION?
4 -- in contrast, shall I use the standard R functions plot(ecdf), there is
no "warning mesage"
plot(ecdf(x$LENGTH), xlab="DEL LENGTH",
ylab="Fraction of DEL", main="DEL", xlim=c(0,500),
col = "dark red")
Thanks a lot !
-- bogdan
Check yours data: outlyers, format, NA's
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Bogdan Tanasa

2018-07-09 05:39:14 UTC

Permalink

Dear Hadley,

thank you for your message : great to her from you. I can see the input and
output files available at :
https://groups.google.com/forum/#!topic/ggplot2/qZzi43CO7nY

nevertheless, I aimed to build a reprex repository, and here the folder
attached (hope it is helpful ... not very sure if all the files inside the
folder are at the best standards '). thanks a lot for your help,

-- bogdan

Post by Hadley Wickham
I would highly recommend that you create a reprex, see
https://www.tidyverse.org/help/ for some details.
Hadley

file <- read.delim("LENGTH", sep="\t", header=T, stringsAsFactors=F)
pdf("display.R.ecdf.LENGTH.pdf", width=10, height=6, paper='special')
plot(ecdf(file$LENGTH), xlab="DEL SIZE",
ylab="fraction of DEL",
main="LENGTH of DEL",
xlim=c(0,500),
col = "dark red", axes = FALSE)
ticks_y <- c(0, 0.2, 0.4, 0.6, 0.8, 1, 1.2, 1.4)
axis(2, at=ticks_y, labels=ticks_y, col.axis="red")
ticks_x <- c(0, 100, 200, 400, 500, 600, 700, 800)
axis(1, at=ticks_x, labels=ticks_x, col.axis="blue")
dev.off()
BREAKS = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500,
1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000)
barfill <- "#4271AE"
barlines <- "#1F3552"
pdf("display.ggplot2.ecdf.LENGTH.pdf", width=10, height=6,
paper='special')
ggplot(file, aes(LENGTH)) +
stat_ecdf(geom = "point", colour = barlines, fill = barfill) +
scale_x_continuous(name = "LENGTH of DEL",
breaks = BREAKS,
limits=c(0, 500)) +
scale_y_continuous(name = "FRACTION") +
ggtitle("ECDF of LENGTH") +
theme_bw() +
theme(legend.position = "bottom", legend.direction =
"horizontal",
legend.box = "horizontal",
legend.key.size = unit(1, "cm"),
axis.title = element_text(size = 12),
legend.text = element_text(size = 9),
legend.title=element_text(face = "bold", size = 9))
dev.off()
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about ECDF display in ggplot2
<http://groups.google.com/group/ggplot2/t/a99ce2e3708eee76?utm_source=digest&utm_medium=email>
Dear all,
I would appreciate having your advice/suggestions/comments on the following
1 -- starting from a vector that contains LENGTHS (numerically, the values
are from 1 to 10 000)
BREAKS = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500,
1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000)
ggplot(x, aes(LENGTH)) +
stat_ecdf(geom = "point") +
scale_x_continuous(name = "LENGTH of DEL",
breaks = BREAKS,
limits=c(0, 500))
3 -- I am getting the following warning message : "Warning message: Removed
109 rows containing non-finite values (stat_ecdf)."
The question is : are these 109 values removed from VISUALIZATION as i set
up the "limits", or are these 109 values removed from statistical
CALCULATION?
4 -- in contrast, shall I use the standard R functions plot(ecdf), there is
no "warning mesage"
plot(ecdf(x$LENGTH), xlab="DEL LENGTH",
ylab="Fraction of DEL", main="DEL", xlim=c(0,500),
col = "dark red")
Thanks a lot !
-- bogdan
Check yours data: outlyers, format, NA's
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