Related
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")
This is not so much a coding as general approach call for help ;-) I prepared a table containing taxonomic information about organisms. But I want to use the "names" of these organisms, so no values or anything where you could compute a distance or clustering with (this is also all the information I have). I just want to use these factors to create a plot that shows the relationship. My data looks like this:
test2<-structure(list(genus = structure(c(4L, 2L, 7L, 8L, 6L, 1L, 3L,
5L, 5L), .Label = c("Aminobacter", "Bradyrhizobium", "Hoeflea",
"Hyphomonas", "Mesorhizobium", "Methylosinus", "Ochrobactrum",
"uncultured"), class = "factor"), family = structure(c(4L, 1L,
2L, 3L, 5L, 6L, 6L, 6L, 6L), .Label = c("Bradyrhizobiaceae",
"Brucellaceae", "Hyphomicrobiaceae", "Hyphomonadaceae", "Methylocystaceae",
"Phyllobacteriaceae"), class = "factor"), order = structure(c(1L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("Caulobacterales",
"Rhizobiales"), class = "factor"), class = structure(c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "Alphaproteobacteria", class = "factor"),
phylum = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "Proteobacteria", class = "factor")), .Names = c("genus",
"family", "order", "class", "phylum"), class = "data.frame", row.names = c(NA,
9L))
is it necessary to set up artificial values to describe a distance between the levels?
Here is an attempt using data.tree library
First create a string variable in the form:
Proteobacteria/Alphaproteobacteria/Caulobacterales/Hyphomonadaceae/Hyphomonas
library(data.tree)
test2$pathString <- with(test2,
paste(phylum,
class,
order,
family,
genus, sep = "/"))
tree_test2 = as.Node(test2)
plot(tree_test2)
many things can be done after like:
Interactive network:
library(networkD3)
test2_Network <- ToDataFrameNetwork(tree_test2, "name")
simpleNetwork(test2_Network)
or graph styled
library(igraph)
plot(as.igraph(tree_test2, directed = TRUE, direction = "climb"))
check out the vignette
using ggplot2:
library(ggraph)
graph = as.igraph(tree_test2, directed = TRUE, direction = "climb")
ggraph(graph, layout = 'kk') +
geom_node_text(aes(label = name))+
geom_edge_link(arrow = arrow(type = "closed", ends = "first",
length = unit(0.20, "inches"),
angle = 15)) +
geom_node_point() +
theme_graph()+
coord_cartesian(xlim = c(-3,3), expand = TRUE)
or perhaps:
ggraph(graph, layout = 'kk') +
geom_node_text(aes(label = name), repel = T)+
geom_edge_link(angle_calc = 'along',
end_cap = circle(3, 'mm'))+
geom_node_point(size = 5) +
theme_graph()+
coord_cartesian(xlim = c(-3,3), expand = TRUE)
I tried to make the title self-explanatory, but here goes - data first:
dtf <- structure(list(variable = structure(c(1L, 1L, 2L, 2L, 3L, 3L,
4L, 4L, 5L, 5L), .Label = c("vma", "vla", "ia", "fma", "fla"), class = "factor"),
ustanova = structure(c(1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L), .Label = c("srednja škola", "fakultet"), class = "factor"),
`(all)` = c(42.9542857142857, 38.7803203661327, 37.8996138996139,
33.7672811059908, 29.591439688716, 26.1890660592255, 27.9557692307692,
23.9426605504587, 33.2200772200772, 26.9493087557604)), .Names = c("variable",
"ustanova", "(all)"), row.names = c(NA, 10L), class = c("cast_df",
"data.frame"), idvars = c("variable", "ustanova"), rdimnames = list(
structure(list(variable = structure(c(1L, 1L, 2L, 2L, 3L,
3L, 4L, 4L, 5L, 5L), .Label = c("vma", "vla", "ia", "fma",
"fla"), class = "factor"), ustanova = structure(c(1L, 2L,
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L), .Label = c("srednja škola",
"fakultet"), class = "factor")), .Names = c("variable", "ustanova"
), row.names = c("vma_srednja škola", "vma_fakultet", "vla_srednja škola",
"vla_fakultet", "ia_srednja škola", "ia_fakultet", "fma_srednja škola",
"fma_fakultet", "fla_srednja škola", "fla_fakultet"), class = "data.frame"),
structure(list(value = structure(1L, .Label = "(all)", class = "factor")), .Names = "value", row.names = "(all)", class = "data.frame")))
And I'd like to create a dodged barplot, do the coord_flip and put some text labels inside the bars:
ggplot(bar) + geom_bar(aes(variable, `(all)`, fill = ustanova), position = "dodge") +
geom_text(aes(variable, `(all)`, label = sprintf("%2.1f", `(all)`)), position = "dodge") +
coord_flip()
you can see output here.
I reckon I'm asking for something trivial. I want the text labels to "follow" stacked bars. Labels are placed correctly on the y-axis, but how to position them correctly on x-axis?
Is this what you want?
library(ggplot2)
ggplot(bar) +
geom_col(aes(variable, `(all)`, fill = ustanova), position = "dodge") +
geom_text(aes(variable, `(all)`, label = sprintf("%2.1f", `(all)`), group = ustanova),
position = position_dodge(width = .9)) +
coord_flip()
The key is to position = position_dodge(width = .9) (where .9 is the default width of the bars) instead of position = "dodge", which is just a shortcut without any parameter. Additionally you have to set the group=ustanova aesthetic in geom_text to dodge the labels by ustanova (A second option would be to make fill = ustanova a global aesthetic via ggplot(bar, aes(fill = ustanova))
In ggplot2_2.0.0 you find several examples in ?geom_text on how to position geom_text on dodged or stacked bars (the code chunk named "# Aligning labels and bars"). The Q&A What is the width argument in position_dodge? provides a more thorough description of the topic.
I'm trying to plot a network graph using the d3Network package. I tried organizing the data to match the instructions as they appear on the package website (and help page), but I still get a blank web page. Can anyone spot what I'm doing wrong?
library(d3Network)
g.top3000 <- structure(list(from = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 3L, 3L, 3L, 4L, 4L, 5L), .Label = c("afghanistan", "attack",
"people", "pres_bush", "taliban"), class = "factor"), to = structure(c(4L,
1L, 5L, 2L, 3L, 1L, 5L, 2L, 3L, 5L, 2L, 3L, 2L, 3L, 3L), .Label = c("people",
"taliban", "united_states", "attack", "pres_bush"), class = "factor"),
weight = c(4, 3, 2, 6, 5, 5, 2, 3, 6, 1, 1, 5, 2, 4, 4)), .Names = c("from",
"to", "weight"), row.names = c(NA, -15L), class = "data.frame")
top3000.nodes <- structure(list(name = structure(1:5, .Label = c("afghanistan",
"attack", "people", "pres_bush", "taliban"), class = "factor"),
id = c(1, 1, 1, 2, 2)), .Names = c("name", "id"), row.names = c(NA,
-5L), class = "data.frame")
d3ForceNetwork(Links = g.top3000, Nodes = top3000.nodes, Source = "from", Target = "to",
Value = "weight", NodeID = "name", Group = "id", width = 800, height = 400, opacity = 0.9,
file = "projekt2_terror_news_force.html")
Plotting a simple graph works just fine
d3SimpleNetwork(g.top3000, width = 800, height = 400, fontsize = 12, linkDistance = 200,
file = "projekt2_terror_news.html")
That's because
No entry of "united status" in the node list.
You may need to use numeric index instead of node name.
# add entry "united status"
top3000.nodes <- rbind(top3000.nodes, data.frame(name = "united_states", id = 3))
# from name to index
g.top3000$from2 <- sapply(as.character(g.top3000$from), function(x) which(x == top3000.nodes$name))-1
g.top3000$to2 <- sapply(as.character(g.top3000$to), function(x) {
i <- which(x == top3000.nodes$name)
if (length(i)) i else NA
}) -1
# use indices in "from2" and "to2"
d3ForceNetwork(Links = g.top3000, Nodes = top3000.nodes, Source = "from2", Target = "to2",
Value = "weight", NodeID = "name", Group = "id", width = 800, height = 400, opacity = 0.4,
file = "projekt2_terror_news_force.html", linkDistance = 200)
I tried to make the title self-explanatory, but here goes - data first:
dtf <- structure(list(variable = structure(c(1L, 1L, 2L, 2L, 3L, 3L,
4L, 4L, 5L, 5L), .Label = c("vma", "vla", "ia", "fma", "fla"), class = "factor"),
ustanova = structure(c(1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L), .Label = c("srednja škola", "fakultet"), class = "factor"),
`(all)` = c(42.9542857142857, 38.7803203661327, 37.8996138996139,
33.7672811059908, 29.591439688716, 26.1890660592255, 27.9557692307692,
23.9426605504587, 33.2200772200772, 26.9493087557604)), .Names = c("variable",
"ustanova", "(all)"), row.names = c(NA, 10L), class = c("cast_df",
"data.frame"), idvars = c("variable", "ustanova"), rdimnames = list(
structure(list(variable = structure(c(1L, 1L, 2L, 2L, 3L,
3L, 4L, 4L, 5L, 5L), .Label = c("vma", "vla", "ia", "fma",
"fla"), class = "factor"), ustanova = structure(c(1L, 2L,
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L), .Label = c("srednja škola",
"fakultet"), class = "factor")), .Names = c("variable", "ustanova"
), row.names = c("vma_srednja škola", "vma_fakultet", "vla_srednja škola",
"vla_fakultet", "ia_srednja škola", "ia_fakultet", "fma_srednja škola",
"fma_fakultet", "fla_srednja škola", "fla_fakultet"), class = "data.frame"),
structure(list(value = structure(1L, .Label = "(all)", class = "factor")), .Names = "value", row.names = "(all)", class = "data.frame")))
And I'd like to create a dodged barplot, do the coord_flip and put some text labels inside the bars:
ggplot(bar) + geom_bar(aes(variable, `(all)`, fill = ustanova), position = "dodge") +
geom_text(aes(variable, `(all)`, label = sprintf("%2.1f", `(all)`)), position = "dodge") +
coord_flip()
you can see output here.
I reckon I'm asking for something trivial. I want the text labels to "follow" stacked bars. Labels are placed correctly on the y-axis, but how to position them correctly on x-axis?
Is this what you want?
library(ggplot2)
ggplot(bar) +
geom_col(aes(variable, `(all)`, fill = ustanova), position = "dodge") +
geom_text(aes(variable, `(all)`, label = sprintf("%2.1f", `(all)`), group = ustanova),
position = position_dodge(width = .9)) +
coord_flip()
The key is to position = position_dodge(width = .9) (where .9 is the default width of the bars) instead of position = "dodge", which is just a shortcut without any parameter. Additionally you have to set the group=ustanova aesthetic in geom_text to dodge the labels by ustanova (A second option would be to make fill = ustanova a global aesthetic via ggplot(bar, aes(fill = ustanova))
In ggplot2_2.0.0 you find several examples in ?geom_text on how to position geom_text on dodged or stacked bars (the code chunk named "# Aligning labels and bars"). The Q&A What is the width argument in position_dodge? provides a more thorough description of the topic.