lollipops | style mutation diagrams for annotating genetic variations | Genomics library
kandi X-RAY | lollipops Summary
lollipops is a Go library typically used in Artificial Intelligence, Genomics applications. lollipops has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.
A simple 'lollipop' mutation diagram generator that tries to make things simple and easy by automating as much as possible. It uses the UniProt REST API and/or Pfam API to automate translation of Gene Symbols and lookup domain/motif features for display. If variant changes are provided, it will also annotate them to the diagram using the "lollipops" markers that give the tool it's name.
Support
Quality
Security
License
Reuse
Support
Quality
Security
License
Reuse
Support
lollipops has a low active ecosystem.
It has 153 star(s) with 56 fork(s). There are 16 watchers for this library.
It had no major release in the last 12 months.
There are 2 open issues and 45 have been closed. On average issues are closed in 18 days. There are 2 open pull requests and 0 closed requests.
It has a neutral sentiment in the developer community.
The latest version of lollipops is v1.5.3
lollipops Support
Best in #Genomics
Average in #Genomics
lollipops Support
Best in #Genomics
Average in #Genomics
Quality
lollipops has 0 bugs and 0 code smells.
lollipops Quality
Best in #Genomics
Average in #Genomics
lollipops Quality
Best in #Genomics
Average in #Genomics
Security
lollipops has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
lollipops code analysis shows 0 unresolved vulnerabilities.
There are 0 security hotspots that need review.
lollipops Security
Best in #Genomics
Average in #Genomics
lollipops Security
Best in #Genomics
Average in #Genomics
License
lollipops is licensed under the GPL-3.0 License. This license is Strong Copyleft.
Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.
lollipops License
Best in #Genomics
Average in #Genomics
lollipops License
Best in #Genomics
Average in #Genomics
Reuse
lollipops releases are available to install and integrate.
Installation instructions, examples and code snippets are available.
lollipops Reuse
Best in #Genomics
Average in #Genomics
lollipops Reuse
Best in #Genomics
Average in #Genomics
Top functions reviewed by kandi - BETA
kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample Here
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample Here
lollipops Key Features
Jay JJ, Brouwer C (2016) Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine. PLoS ONE 11(8): e0160519. doi: 10.1371/journal.pone.0160519.
lollipops Examples and Code Snippets
No Code Snippets are available at this moment for lollipops.
Community Discussions
Trending Discussions on lollipops
How to link traces between subplots in R Plotly with shared Y axis so that hoverinfo appears on both?
I am having problems with the css highlighting text
lollipop plot with sorting within group
Trending Discussions on lollipops
QUESTION
How to link traces between subplots in R Plotly with shared Y axis so that hoverinfo appears on both?
Asked 2021-Nov-23 at 07:38
I've managed to create a figure made of two subplots which are horizontal bar charts (lollipops), side-by-side, with a shared Y-axis:
However, I'd like each pair of horizontal lollipops to be linked between them so that when you hover over one the hovertemplate info is shown for both instead of just one. Is there a way to do this using Plotly R, perhaps a custom JS function or something like that? I assume it's not easily possible using the legend group option.
So far I've tried these two approaches and none of them do what I want: R plotly link subplots so that multiple tooltips shown on hover How to facet a plot_ly() chart?
Here's a link to my data: https://www.dropbox.com/s/g6kqq4z2y6nsk2g/plotly_data.RData?dl=0
And my code so far:
custom_hover_t <- "%{x:.2f}%"
custom_hover_c <- "%{x:.2f}%"
t <- plot_ly(data = datos) %>%
#Barras tamaño
add_trace(x = ~T2019, y = ~EjeX,
type = 'bar',
width = 0.02,
marker = list(color = ~color),
orientation = "h",
hoverlabel = list(bordercolor="white"),
hovertemplate = custom_hover_t
) %>%
add_trace(x = ~T2019, y = ~EjeX,
type = 'scatter',mode = "markers",
marker = list(color = ~color, size = 7),
hoverlabel = list(bordercolor="white"),
hovertemplate = custom_hover_t
) %>%
plotly::layout(
xaxis = list(title = NULL,
autorange = T,
zeroline = T,
showline = F,
autotick = FALSE,
tickmode = "array",
showgrid = T,
showticklabels = F,
titlefont = list(color="transparent")
),
yaxis = list(title = NULL,
visible = FALSE,
autorange = TRUE,
visible = FALSE,
zeroline = FALSE,
showline = F,
showgrid = FALSE,
ticklen = 0,
titlefont = list(color="transparent")
), #para mostrar solo 2 decimales al hacer hover en un punto
showlegend = F#,
#margin = list(l = 1)
)
c <- plot_ly(data = datos) %>%
#Barras tamaño
add_trace(x = ~CambioRel, y = ~EjeX,
type = 'bar',
width = 0.02,
marker = list(color = ~color),
orientation = "h",
hoverlabel = list(bordercolor="white"),
hovertemplate = custom_hover_c
) %>%
add_trace(x = ~CambioRel, y = ~EjeX,
type = 'scatter',mode = "markers",
marker = list(color = ~color, size = 7),
hoverlabel = list(bordercolor="white"),
hovertemplate = custom_hover_c
) %>%
plotly::layout(
xaxis = list(title = NULL,
autorange = T,
zeroline = T,
showline = F,
autotick = FALSE,
tickmode = "array",
#tickvals = ~Etiqueta,
showgrid = T,
showticklabels = F,
titlefont = list(color="transparent")
),
yaxis = list(title = NULL,
visible = FALSE,
autorange = TRUE,
visible = FALSE,
zeroline = FALSE,
showline = F,
showgrid = FALSE,
#ticks = "outside",
#ticksuffix = ticks_pct(),
#showticklabels = TRUE,
ticklen = 0,
titlefont = list(color="transparent")
), #para mostrar solo 2 decimales al hacer hover en un punto
showlegend = F#,
#margin = list(l = 1)
)
fig <- subplot(t, c, shareY = TRUE)
fig
I'd really really appreciate any help you can give me
ANSWER
Answered 2021-Nov-23 at 07:38Shared hoverinfo across subplots is not yet available in plotly.js.
However, you could use hovermode = 'y unified' in a single plot across different traces:
library(plotly)
fig <- plot_ly()
fig <- fig %>% add_trace(x = ~2:4, y = ~4:6, text = ~LETTERS[4:6], name = "yaxis data", mode = "lines+markers", type = "scatter", hovertemplate = "%{text}")
fig <- fig %>% add_trace(x = ~4:6, y = ~4:6, name = "yaxis 2 data", mode = "lines+markers", type = "scatter")
fig <- fig %>% add_trace(x = ~6:8, y = ~4:6, name = "omit_hoverinfo", mode = "lines+markers", type = "scatter", hoverinfo='skip')
fig <- fig %>% layout(
hovermode = 'y unified' # alternativ: hovermode = 'y'
)
fig
QUESTION
I am having problems with the css highlighting text
Asked 2021-Feb-24 at 13:04
I am having problems with the css side of the hypertext link, the strings that transport you to the other pages of the website, they are not highlighting when I hover over the message, when it comes to the stuff, I cannot see the problems with the code, could i have some help with this please?:
ul {
list-style-type: none;
margin: 0;
padding: 0;
overflow: hidden;
background-color: #333;
}
li {
float: left;
}
li a {
color: white;
text-align: center;
padding: 14px 16px;
text-decoration: none;
hover: red;
}
a {
color: white;
}
}
a:hover {
color: red;
}ANSWER
Answered 2021-Feb-24 at 13:04- You have a typo,
u1instead oful - You have too many definitions of A so the hover is ignored, I removed
a { color: white; } - Unnecessary inline list types on the LIs
- Don't use float and br when not using float and br does the same. I removed
li { float: left; }and
ul {
list-style-type: none;
margin: 0;
padding: 0;
overflow: hidden;
background-color: #333;
}
li a {
color: white;
text-align: center;
padding: 14px 16px;
text-decoration: none;
}
li a:hover {
color: red;
}QUESTION
lollipop plot with sorting within group
Asked 2020-May-05 at 18:30
I am trying to create a lollipop plot with a dataset that looks something like this:
set.seed(123)
example_df <- data.frame(strategy = as.factor(rep(LETTERS[1:5], each = 2)),
mt_equip = as.factor(rep(c('r', 'v'), times = 5)),
cc = as.factor(c('cc', 'cc', 'no_cc', 'no_cc', 'part_cc', 'part_cc', 'cc', 'cc', 'no_cc', 'no_cc')),
vt = as.factor(c(rep('d10', 4), rep('d1+d10', 2), rep('d1', 4))),
model_ouput = rnorm(10)
)
example_df
strategy mt_equip cc vt model_ouput
1 A r cc d10 -0.56047565
2 A v cc d10 -0.23017749
3 B r no_cc d10 1.55870831
4 B v no_cc d10 0.07050839
5 C r part_cc d1+d10 0.12928774
6 C v part_cc d1+d10 1.71506499
7 D r cc d1 0.46091621
8 D v cc d1 -1.26506123
9 E r no_cc d1 -0.68685285
10 E v no_cc d1 -0.44566197
My goal is to make a lollipop plot so that:
- they are grouped and colored by
cc, withmt_equipas theshapespecification. - within each
cccategory, the lollipops are sorted from lowest to highest. - the lollipops should be separated and not entangled like in the figure shown.
I tried the geom_lollipop() option from the ggalt package as follows:
library(ggalt)
option2 <- ggplot(data = example_df,
aes(x = reorder(cc, model_ouput))) +
geom_lollipop(aes(y = model_ouput,
shape = mt_equip,
color = cc),
size = 5) +
scale_shape_manual(values = c(21, 24))
plot(option2)
This is what I get:
How can I:
- disentangle the lollipops so that each one stands alone within the
ccgroup? - sort the disentangled lollipops in (1) from lowest to highest? I tried
reorderbut it did not produce the designed effect as shown in the image. - make the bars hollow for post-processing with color and stroke?
Thank you for your help.
ANSWER
Answered 2020-May-05 at 18:30Upon taking a few hints from @GregorThomas, I finally solved the problem with the following code:
library(ggalt)
library(dplyr)
library(tidyr)
set.seed(123)
example_df <- data.frame(strategy = as.factor(rep(LETTERS[1:5], each = 2)),
mt_equip = as.factor(rep(c('r', 'v'), times = 5)),
cc = as.factor(c('cc', 'cc', 'no_cc', 'no_cc', 'part_cc', 'part_cc', 'cc', 'cc', 'no_cc', 'no_cc')),
vt = as.factor(c(rep('d10', 4), rep('d1+d10', 2), rep('d1', 4))),
model_ouput = rnorm(10)
)
#the strategy variable is not unique so we make it so but combining two cols
example_df_mod <- example_df %>%
unite(col = 'strategy', c(strategy, mt_equip), remove = F)
#make lollipop plot grouped by cc and sorted within each group
option2 <- example_df_mod %>%
group_by(cc) %>%
arrange(model_ouput, .by_group = T) %>%
ggplot(aes(group = cc)) +
geom_lollipop(aes(x = order(cc, model_ouput),
y = model_ouput,
shape = mt_equip,
color = cc),
size = 5)
plot(option2)
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install lollipops
Head over to the Releases to download the latest version for your system in a simple command-line executable. If you already have Go installed and want the bleeding edge, just go get -u github.com/joiningdata/lollipops to download the latest version.
Support
Please submit your bugs and features requests via the Issues tab. Be sure to search closed issues before submitting a new one in case the issue has been previously discussed. Pull Requests are welcome, but please create an issue beforehand to discuss significant changes. Code contributions are expected to be properly formatted with go fmt, and generally adhere to the standard Golang review guidelines.
Find more information at:
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesExplore Kits - Develop, implement, customize Projects, Custom Functions and Applications with kandi kits
Save this library and start creating your kit
Share this Page
Reuse Trending Solutions