Draw radial background in ggplot - r

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:

Related

ggplot 'race track' plot with polar_coord + points

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()

Credibility interval with respect two factors using ggplot2 in r

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")

Mosaic Plot does not fit

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)))

Order x axis after factor variable with fewer levels

I have the following data frame:
structure(list(Substance = c("Cefotaxime", "Cefepim", "Chloramphenicol",
"Sulfamethoxazole", "Ampicillin", "Ampicillin", "Tetracycline",
"Cefotaxime", "Trimethoprim", "Cefepim", "Cefepim", "Sulfamethoxazole",
"Ceftazidime", "Nalidixic acid", "Cefepim", "Ceftazidime", "Ampicillin",
"Ceftazidime", "Cefotaxime", "Ceftazidime"), Species = c("Cattle",
"Chicken", "Cattle", "Cattle", "Cattle", "Cattle", "Cattle",
"Pig", "Cattle", "Cattle", "Horse", "Horse", "Pig", "Cattle",
"Pig", "Pig", "Cattle", "Cattle", "Pig", "Horse"), gene = c("AmpC",
"blaCMY-2", "blaSHV-12", "blaCMY-2", "AmpC", "blaCMY-2", "blaCMY-2",
"AmpC", "blaSHV-12", "blaSHV-12", "blaCTX-M Group 1", "blaCTX-M Group 1",
"AmpC", "blaSHV-12", "blaCTX-M-15", "blaCTX-M-15", "AmpC", "AmpC",
"blaCMY-2", "AmpC"), n = c(3, 6, 1, 1, 3, 1, 1, 3, 1, 1, 1, 1,
3, 1, 1, 1, 1, 1, 1, 1), group = c(8L, 3L, 5L, 9L, 8L, 9L, 9L,
13L, 5L, 5L, 2L, 2L, 13L, 5L, 16L, 16L, 7L, 7L, 15L, 1L), value = c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L)), class = c("tbl_df", "tbl", "data.frame"), row.names = c(NA,
-20L), .Names = c("Substance", "Species", "gene", "n", "group",
"value"))
And I have this plot:
gene_palette <- c("AmpC" = "#b2182b",
"blaCMY-2" = "#ef8a62",
"blaCTX-M-15" = "#fddbc7",
"blaCTX-M Group 1" = "#d1e5f0",
"blaSHV-12" = "#67a9cf",
"ESBL" = "#2166ac")
library(ggplot2)
ggplot(test, aes(factor(group), Substance, fill = gene))+
geom_point(pch = 21, size = 5)+
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))+
scale_fill_manual(values = gene_palette)+
theme_classic()
This produces the following plot:
Is there a way to sort the order of "groups" on the x-axis so that each gene will be next to eachother on the x axis, in the order listed in the legend? This way, the color for each gene type will be next to each other.
I tried the solutions presented here, but since the factor variables in "gene" is fewer and doesn't match the ones in "group", that didn't work (introduced NA's)
ggplot(test, aes(factor(group,
levels = unique(test[order(test$gene, test$group), "group", drop = TRUE])),
Substance, fill = gene))+
geom_point(pch = 21, size = 5)+
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))+
scale_fill_manual(values = gene_palette)+
theme_classic()

geom_point not really hollow, error bar overlaps

This might seem a really stupid mistake on my part but whenever I specify geom_point depending on a factor and choose a hollow point and a solid point (shapes 1 and 19), and plot error bars, it crosses the point.
Here are my data frames:
> dput(head(allbins.sum))
structure(list(T = c(0L, 0L, 10L, 10L, 20L, 20L), treatment = structure(c(1L,
2L, 1L, 2L, 1L, 2L), .Label = c("control bead", "dP bead"), class = "factor"),
N = c(3, 3, 3, 3, 3, 3), cellsBase = c(0, 0, 0.013028995209506,
0.135599858885737, -0.0130289952095061, 0.759359209760127
), sd = c(0, 0, 0.0597063567767786, 0.0469731690178533, 0.0983667566897066,
0.183436089048999), se = c(0, 0, 0.034471481157405, 0.0271199717771474,
0.0567920734541125, 0.105906875391532), ci = c(0, 0, 0.148318812500416,
0.116687820597672, 0.244356569875469, 0.455680506502609),
bin = c("BinA", "BinA", "BinA", "BinA", "BinA", "BinA")), .Names = c("T",
"treatment", "N", "cellsBase", "sd", "se", "ci", "bin"), row.names = c(NA,
6L), class = "data.frame")
> dput(head(allbins.fitdata))
structure(list(wellvidbin = structure(c(1L, 1L, 1L, 1L, 1L, 1L
), .Label = c("A1-002-BinA", "A1-002-BinB", "A1-002-BinC", "A1-031-BinA",
"A1-031-BinB", "A1-031-BinC", "A3-004-BinA", "A3-004-BinB", "A3-004-BinC",
"B1-032-BinA", "B1-032-BinB", "B1-032-BinC", "B4-026-BinA", "B4-026-BinB",
"B4-026-BinC", "C4-027-BinA", "C4-027-BinB", "C4-027-BinC"), class = "factor"),
treatment = structure(c(2L, 2L, 2L, 2L, 2L, 2L), .Label = c("control bead",
"dP bead"), class = "factor"), wellvid = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("A1-002", "A1-031", "A3-004",
"B1-032", "B4-026", "C4-027"), class = "factor"), bin = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("BinA", "BinB", "BinC"), class = "factor"),
T = c(0L, 10L, 20L, 30L, 40L, 50L), T.factor = structure(1:6, .Label = c("0",
"10", "20", "30", "40", "50", "60"), class = "factor"), cells = c(7L,
11L, 26L, 27L, 28L, 36L), cellsS = c(-1.36568429306349, -1.20296446240061,
-0.592765097414793, -0.552085139749072, -0.511405182083351,
-0.185965520757582), cellsBase = c(0, 0.162719830662884,
0.772919195648701, 0.813599153314422, 0.854279110980143,
1.17971877230591), treatT = structure(c(2L, 4L, 6L, 8L, 10L,
12L), .Label = c("control bead.0", "P bead.0", "control bead.10",
"P bead.10", "control bead.20", "P bead.20", "control bead.30",
"P bead.30", "control bead.40", "P bead.40", "control bead.50",
"P bead.50", "control bead.60", "P bead.60"), class = "factor"),
fit = c(0.0285939715820639, 0.304399288764407, 0.58020460594675,
0.856009923129092, 1.13181524031144, 1.40762055749378), se.fit = c(0.157415367032567,
0.132348142293459, 0.114707848741265, 0.108190467052118,
0.114707848741265, 0.132348142293459), upr = c(0.337128090965895,
0.563801647659587, 0.805031989479629, 1.06806323855124, 1.35664262384431,
1.66702291638896), lwr = c(-0.279940147801767, 0.0449969298692267,
0.35537722241387, 0.643956607706942, 0.906987856778556, 1.1482181985986
)), .Names = c("wellvidbin", "treatment", "wellvid", "bin",
"T", "T.factor", "cells", "cellsS", "cellsBase", "treatT", "fit",
"se.fit", "upr", "lwr"), class = c("data.table", "data.frame"
), row.names = c(NA, -6L), .internal.selfref = <pointer: 0x0000000000100788>)
And the code:
ggplot(data=allbins.sum, aes(x=T, y=cellsBase, shape=treatment)) + geom_point(size=5, aes(shape=treatment))+
geom_errorbar(aes(ymin=cellsBase-se, ymax=cellsBase+se), width=2, size=1) +
geom_smooth(data=allbins.fitdata, size=1, aes(y=fit, ymin=lwr, ymax=upr),
color="black", method="lm", stat="identity", alpha=0.2)+
facet_grid(bin~.) +
scale_shape_manual(values=c(1, 19))
This gives me this plot:
Any hints on how to have the hollow circles to be hollowed?
I also tried specifying geom_shape (aes(fill=treatment) and then scale_fill_manual but then it is also applied to my geom_smooth
Thanks for the help!
If you mean that you don't want the line of the error bar to be visible through the 'hollow' points, then plot geom_errorbar first, then plot geom_point second, with solid fill, so it will overlay the error bar.
ggplot(data=allbins.sum, aes(x=T, y=cellsBase)) +
# plotting this first
geom_errorbar(aes(ymin=cellsBase-se, ymax=cellsBase+se), width=2, size=1) +
# plotting this second, with a hollow fillable shape, and black outline
geom_point(size=5, shape = 21, color='black',
aes(fill = treatment)) +
# solid black and solid white fill for the points
scale_fill_manual(values = c('black', 'white')) +
theme_bw()
(The data you posted only has these points for allbins.sum, and the code for allbins.fitdata has an error, so no error bars on this plot)

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