I have problem ploting credibility interval like this:
My data structure is following，L1,L2,M,U1,U2 stand for 0.025quant,0.25quant,0.5quant,0.75quant,0.975quant,respectively.
`
structure(list(approach = structure(c(1L, 2L, 1L, 2L, 1L, 2L), class = "factor", .Label = c("INLA",
"rjags")), param = structure(c(1L, 2L, 3L, 1L, 2L, 3L), class = "factor", .Label = c("alpha",
"beta", "sig2")), L1 = c(0.0844546867936143, 1.79242348175439,
0.163143886545317, 0.0754165380733685, 1.79067991488052, 3.66675821267498
), L2 = c(0.60090835904286, 1.95337968870806, 0.898159977552433,
0.606017177641373, 1.95260448314298, 4.07080184844179), M = c(0.870204161297956,
2.03768437879748, 2.20651061559405, 0.87408237273113, 2.03725552264872,
4.32531027636171), U2 = c(1.13905085248391, 2.12210930874551,
4.26836270504725, 1.66260576926063, 2.28900567640091, 5.10063756831338
), U1 = c(1.65214011950274, 2.28396345192398, 4.9109804477583,
1.1450384685802, 2.12117799328209, 4.55657971279654), AP = structure(c(1L,
4L, 5L, 2L, 3L, 6L), .Label = c("INLA.alpha", "rjags.alpha",
"INLA.beta", "rjags.beta", "INLA.sig2", "rjags.sig2"), class = "factor")), .Names = c("approach",
"param", "L1", "L2", "M", "U2", "U1", "AP"), row.names = c(NA,
-6L), class = "data.frame")`
I referenced this answerenter link description here,but 'fill' seems only work for boxplot case.the code I tried so far is:
CI$AP=interaction(CI$approach,CI$param)
p=ggplot(CI,aes(y=AP))+geom_point(aes(x=M))
p=p+geom_segment(aes(x=L1,xend=U1,y=AP,yend=AP))
p=p+geom_segment(aes(x=L2,xend=U2,y=AP,yend=AP),size=1.5)
It is far away from what I want.
Many thanks!
How about the following:
ggplot(df, aes(x = param, y = M, colour = approach)) +
geom_point(position = position_dodge2(width = 0.3), size = 3) +
geom_linerange(
aes(ymin = L2, ymax = U2, x = param),
position = position_dodge2(width = 0.3),
size = 2) +
geom_linerange(
aes(ymin = L1, ymax = U1, x = param),
position = position_dodge2(width = 0.3),
size = 1) +
coord_flip() +
labs(x = "Parameter", y = "Estimate")
Sample data
df <- structure(list(approach = structure(c(1L, 2L, 1L, 2L, 1L, 2L), class = "factor", .Label = c("INLA",
"rjags")), param = structure(c(1L, 2L, 3L, 1L, 2L, 3L), class = "factor", .Label = c("alpha",
"beta", "sig2")), L1 = c(0.0844546867936143, 1.79242348175439,
0.163143886545317, 0.0754165380733685, 1.79067991488052, 3.66675821267498
), L2 = c(0.60090835904286, 1.95337968870806, 0.898159977552433,
0.606017177641373, 1.95260448314298, 4.07080184844179), M = c(0.870204161297956,
2.03768437879748, 2.20651061559405, 0.87408237273113, 2.03725552264872,
4.32531027636171), U2 = c(1.13905085248391, 2.12210930874551,
4.26836270504725, 1.66260576926063, 2.28900567640091, 5.10063756831338
), U1 = c(1.65214011950274, 2.28396345192398, 4.9109804477583,
1.1450384685802, 2.12117799328209, 4.55657971279654), AP = structure(c(1L,
4L, 5L, 2L, 3L, 6L), .Label = c("INLA.alpha", "rjags.alpha",
"INLA.beta", "rjags.beta", "INLA.sig2", "rjags.sig2"), class = "factor")), .Names = c("approach",
"param", "L1", "L2", "M", "U2", "U1", "AP"), row.names = c(NA,
-6L), class = "data.frame")
Related
I'm struggling to get polar_coords to work as I had hoped. I want each item to be represented by a coloured track, with a range of 1:50000. I then wanted to plot points over these tracks at the corresponding locations, with symbols representing the different categories. The points would then be annotated with the id.
Dataframe:
structure(list(item = structure(c(1L, 2L, 2L, 2L, 3L, 4L, 5L,
6L, 7L, 8L, 9L, 10L), .Label = c("AA", "AB", "AC", "AD", "AE",
"BA", "BB", "BC", "BD", "BE"), class = "factor"), location = c(10045L,
12041L, 15035L, 22054L, 19023L, 49411L, 39012L, 3041L, 23065L,
33015L, 42069L, 26859L), category = structure(c(1L, 1L, 2L, 3L,
1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L), .Label = c("X", "Y", "Z"), class = "factor"),
id = structure(c(1L, 8L, 2L, 7L, 6L, 10L, 5L, 1L, 1L, 3L,
4L, 9L), .Label = c("Apple", "Banana", "Cherry", "Grape",
"Mango", "Melon", "Orange", "Pear", "Raspberry", "Strawberry"
), class = "factor")), .Names = c("item", "location", "category",
"id"), class = "data.frame", row.names = c(NA, -12L))
my_data %>%
ggplot(aes(item, location, shape = category, label = id)) +
geom_col(aes(y = Inf), fill = "gray80") +
geom_point(size = 3) +
geom_text(vjust = -1) +
scale_x_discrete(expand = expand_scale(add = c(5,0))) +
coord_polar(theta = "y") +
theme_void()
If you want a break in the middle, you could change the item to a numeric value relating to it's desired position:
my_data %>%
mutate(item_pos = as.numeric(item),
item_pos = item_pos + if_else(item_pos > 5, 1, 0)) %>%
ggplot(aes(item_pos, location, shape = category, label = id)) +
...
Maybe you can work from this:
ggplot(data,aes(x=location, color=id, y=id)) +
geom_linerange(aes(y=id, xmin=0, xmax=50000, color=category), size=2, alpha=0.5) +
geom_point(size=3) +
coord_polar()
I have the following data frame:
structure(list(StepsGroup = structure(c(1L, 1L, 1L, 2L, 2L, 2L,
3L, 3L, 3L), .Label = c("(-Inf,3e+03]", "(3e+03,1.2e+04]", "(1.2e+04, Inf]"
), class = "factor"), GlucoseGroup = structure(c(1L, 2L, 3L,
1L, 2L, 3L, 1L, 2L, 3L), .Label = c("<100", "100-180", ">180"
), class = "factor"), n = c(396L, 1600L, 229L, 787L, 4182L, 375L,
110L, 534L, 55L), freq = c(0.177977528089888, 0.719101123595506,
0.102921348314607, 0.147267964071856, 0.782559880239521, 0.0701721556886228,
0.157367668097282, 0.763948497854077, 0.0786838340486409)), class =
c("grouped_df",
"tbl_df", "tbl", "data.frame"), row.names = c(NA, -9L), vars = "StepsGroup",
labels = structure(list(
StepsGroup = structure(1:3, .Label = c("(-Inf,3e+03]", "(3e+03,1.2e+04]",
"(1.2e+04, Inf]"), class = "factor")), class = "data.frame", row.names =
c(NA, -3L), vars = "StepsGroup", drop = TRUE), indices = list(0:2,
3:5, 6:8), drop = TRUE, group_sizes = c(3L, 3L, 3L), biggest_group_size =
3L)
I would like to create a stacked bar plot, and add a summary of each StepsGroup on top of each bar. So the first group will have 2225, the second 5344 and the third 699.
I am using the following script:
ggplot(d_stepsFastingSummary , aes(y = freq, x = StepsGroup, fill =
GlucoseGroup)) + geom_bar(stat = "identity") +
geom_text(aes(label = sum(n()), vjust = 0))
The part until before the geom_text works, but for the last bit I get the following error:
Error: This function should not be called directly
Any idea how to add the aggregated quantity?
We could create a new dataframe stacked_df which would have sum for each StepsGroup
stacked_df <- df %>% group_by(StepsGroup) %>% summarise(nsum = sum(n))
ggplot(df) +
geom_bar(aes(y = freq, x = StepsGroup, fill= GlucoseGroup),stat = "identity") +
geom_text(data = stacked_df, aes(label = nsum, StepsGroup,y = 1.1))
The labels for the mosaic plot don't fit the screen ( they're partially cut) so id like to move/shift the plot to the right so that the labels fully fit -- tried using ''par'' function but to no avail -- any ideas?
structure(list(Road_Type = structure(c(4L, 4L, 4L, 4L, 4L, 4L
), .Label = c("Roundabout", "One way Street", "Dual Carriageway",
"Single carriageway", "Slip Road"), class = "factor"), Accident_Severity_combined = structure(c(2L,
2L, 2L, 2L, 1L, 2L), .Label = c("Serious", "Slight"), class = "factor")), .Names = c("Road_Type",
"Accident_Severity_combined"), row.names = c(NA, 6L), class = "data.frame")
>
mos <- mosaic(~Road_Type + Accident_Severity_combined, data = uk1, shade = TRUE, legend = TRUE,
labeling_args = list(set_varnames = c(Accident_Severity_combined="Gender", Road_Type="survival"),
highlighting_fill = c("darlblue","red")
labeling=labeling_border(
rot_labels = c(90, 0, 90, 0),
just_labels=c("left","left","right","right"),
tl_varnames = FALSE,
gp_labels = gpar(fontsize = 9)))
this is my dataset:
> dput(dfw)
structure(list(SITE = c("ASPEN", "ASPEN", "BioCON", "DUKE", "Lancaster",
"Merrit Island", "Nevada FACE", "NZ", "ORNL", "PHACE", "BioCON"
), SPECIES = c("A", "AB", "Legume", "PITA", "mixed", "Oak", "desert",
"grassland", "SG", "grassland", "C3forb"), FRr = c(0.197028535345918,
0.296799297050907, 0.195436310641759, 0.152972526753089, 0.0313948973476966,
0.139533057346518, 0.188221278921143, NA, 0.70542764380006, 0.119320766735777,
0.135665667633474), Nupr = c(0.122177669046786, 0.305573297532757,
0.131181914007488, 0.217519050530067, -0.0436788294371676, 0.153632658941404,
-0.00803217169726427, 0.168440046857285, 0.145172439177718, -0.108563178158001,
0.00546006390438276), myc = c("ECM", "ECM", "N-fixing", "ECM",
"ECM", "ECM", "AM", "AM", "AM", "AM", "AM"), SITE_Sps = structure(c(1L,
2L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 3L), .Label = c("Aspen FACE-A",
"Aspen FACE-AB", "BioCON", "BioCON-legumes", "Duke FACE", "Lascaster",
"Florida OTC", "Nevada FACE", "NZ FACE", "ORNL FACE", "PHACE"
), class = "factor")), row.names = c(NA, -11L), vars = list(SITE,
SPECIES, myc), indices = list(0L, 1L, 10L, 2L, 3L, 4L, 5L,
6L, 7L, 8L, 9L), group_sizes = c(1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L), biggest_group_size = 1L, labels = structure(list(
SITE = c("ASPEN", "ASPEN", "BioCON", "BioCON", "DUKE", "Lancaster",
"Merrit Island", "Nevada FACE", "NZ", "ORNL", "PHACE"), SPECIES = c("A",
"AB", "C3forb", "Legume", "PITA", "mixed", "Oak", "desert",
"grassland", "SG", "grassland"), myc = structure(c(2L, 2L,
1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L), .Label = c("am", "ecm",
"ecm+am"), class = "factor")), row.names = c(NA, -11L), class = "data.frame", vars = list(
SITE, SPECIES, myc), .Names = c("SITE", "SPECIES", "myc")), class = c("grouped_df",
"tbl_df", "tbl", "data.frame"), .Names = c("SITE", "SPECIES",
"FRr", "Nupr", "myc", "SITE_Sps"))
I want to draw the same background as in the attached figure, added to my current ggplot code:
ggplot(dfw, aes(FRr, Nupr, group=myc, label = SITE_Sps)) +
geom_point(aes(fill=myc),size=4,shape = 21) +
geom_text() +
geom_hline(yintercept=0) + geom_vline(xintercept = 0) +
geom_abline(intercept = 0, slope = 1, linetype = "longdash")
I guess I should use the function geom_polygon, but I don't really know how to create a dataset to draw all the required segments, including the colour gradient from dark grey to light grey and white.
Perhaps this could be a start?
nlines <-
phis <- seq( 0, 2*pi, by=2*pi/nlines )
rad <- 999
xs <- rad * cos( phis )
ys <- rad * sin( phis )
Here is a way using geom_polygon:
nlines <- 25
inc <- pi/(nlines)
phis <- seq( -pi/2, by=inc, length.out = nlines )
rad <- 1
#Create the triangles
points <- lapply(phis, function(a) {
x <-c(0, rad*cos(a), rad*cos(a+inc),0, -rad*cos(a), -rad*cos(a+inc))
y <-c(0, rad*sin(a), rad*sin(a+inc),0, rad*sin(a), rad*sin(a+inc))
g <-c(a,a,a,a,a,a) # used for grouping
data.frame(x,y,g)
})
#Create a data.frame to be used on ggplot
bckg <- do.call(rbind,points)
#You need to set the data for each geometry as we have more than one dataset
ggplot(mapping=aes(FRr, Nupr, group=myc)) +
#Draw the background
geom_polygon(data=bckg,aes(x=x,y=y,group=g,alpha=g), fill = "gray50")+
geom_point(data=dfw, aes(FRr, Nupr, group=myc, fill=myc),size=4,shape = 21) +
geom_text(data=dfw, aes(FRr, Nupr, group=myc, label = SITE_Sps), nudge_y = -0.02) +
geom_hline(data=dfw,yintercept=0) + geom_vline(data=dfw,xintercept = 0) +
geom_abline(data=dfw,intercept = 0, slope = 1, linetype = "longdash")+
#We need to define a scale in ourder to deal with out of boundary points on the background
scale_x_continuous(limits = c(-0.2,0.4), oob=function(x, rg) x)+
scale_y_continuous(limits = c(-0.2,0.4), oob=function(x, rg) x)+
scale_alpha_continuous(guide="none", range=c(1.0,0))+
theme(panel.background = element_blank())
Here is the plot:
I have an R dataframe data (made with dplyr) that I'm trying to plot with ggplot():
require(dplyr)
data <- structure(list(gGroup = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L), .Label = c("MC", "R", "UC"), class = "factor"),
Episode = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L), .Label = c("Morning", "Day", "Night", "24 hour"
), class = "factor"), variable = c("HF", "HF", "LF", "LF",
"HF", "HF", "LF", "LF", "HF", "HF", "LF", "LF"), parameter = c("RR",
"RT", "RR", "RT", "RR", "RT", "RR", "RT", "RR", "RT", "RR",
"RT"), mean = c(3.90575222833804, 4.24572828952087, 5.14491629837998,
3.88189313775535, 4.02908403079823, 3.91129824615597, 4.73913642980089,
3.63973850905423, 4.66445796048274, 4.21723744674943, 5.57765585365275,
4.01444148455851), sd = c(1.09129154084895, 1.43102672123806,
1.17782114274004, 1.33381488706382, 1.33497319178289, 1.22259231099975,
1.33329948427898, 1.09625319168102, 1.19876558625356, 1.73746797295816,
1.05862249404741, 1.91144835753868), se = c(0.199241664579179,
0.261268538538247, 0.215039736195078, 0.243520167060353,
0.471984298305965, 0.432251656867227, 0.471392553343098,
0.387584032867524, 0.215304655178374, 0.312058460044998,
0.190134212775724, 0.343306259564318)), .Names = c("gGroup",
"Episode", "variable", "parameter", "mean", "sd", "se"), class = c("grouped_df",
"tbl_df", "tbl", "data.frame"), row.names = c(NA, -12L), drop = TRUE, indices = list(
0:1, 2:3, 4:5, 6:7, 8:9, 10:11), group_sizes = c(2L, 2L,
2L, 2L, 2L, 2L), biggest_group_size = 2L, labels = structure(list(
gGroup = structure(c(1L, 1L, 2L, 2L, 3L, 3L), .Label = c("MC",
"R", "UC"), class = "factor"), Episode = structure(c(2L,
2L, 2L, 2L, 2L, 2L), .Label = c("Morning", "Day", "Night",
"24 hour"), class = "factor"), variable = c("HF", "LF", "HF",
"LF", "HF", "LF")), .Names = c("gGroup", "Episode", "variable"
), class = "data.frame", row.names = c(NA, -6L)))
Currently I'm using the following code to plot:
require(ggplot2)
require(ggthemes)
pd <- position_dodge(width=0.9)
p <- ggplot(data, aes(x = gGroup, y = mean, fill = variable)) +
facet_grid(parameter~Episode) +
geom_bar(stat="identity", position=pd) +
geom_errorbar(aes(ymin = mean-se, ymax = mean+se), width = .3, position=pd) +
theme_hc() + scale_fill_hc() +
labs(y = "Logit transform of spectral power (m/s2), mean±SE", x= NULL)
ann_text <- data.frame(gGroup = "MC", mean = 6, variable = "LF", parameter = "RR", Episode = "Day")
p + geom_text(aes(ymax = 6.5, width = .2), data = ann_text, label="*", position=pd)
This gives me the following plot:
I'm quite satisfied with the result, but as you can see the asterisk isn't aligned correctly. I looked it up online, and I read this and this and the manual.
Everyone I see the suggestions to use position=position_dodge(width=0.9), but this doesn't help for me. I tried hjust to maybe move the asterisk to the right position, but that's of no use either. Funny thing is that my error bars are aligned correctly.
I feel like I'm overlooking something very simple, but I cannot figure out what it is.
I'm using R 3.1.3 on OSX 10.10.2, and loading the newest versions of ggplot2 and ggthemes.
In order for position_dodge to work, there needs to be a reason to dodge. That is you need to change the ann_text appropriately with variable = c("LF", "HF"), so that there is a reason to dodge. Then just define the label appropriately. Below I assume you just want the * over the LF bar.
ann_text <- data.frame(gGroup = rep("MC",2),
mean = 6,
variable = c("LF", 'HF'),
label = c("*", ""),
parameter = "RR",
Episode = "Day")
p + geom_text(aes(ymax = 6.5, width = .2, label = label), data = ann_text, position=pd)