I need to plot General transit Feed Specification (GTFS) object routes and their frequencies. For this purpose I have run the following code from the package manual https://cran.r-project.org/web/packages/tidytransit/tidytransit.pdf
to get some practice. But although the code is taken from the manual, I do get the error below. Is there anyone who can clarify this issue and show me an alternative way to perform spatial analysis?
library(tidytransit)
local_gtfs_path <- system.file("extdata",
"google_transit_nyc_subway.zip",
package = "tidytransit")
nyc <- read_gtfs(local_gtfs_path,
local=TRUE)
plot(nyc)
Error in UseMethod("inner_join") :
no applicable method for 'inner_join' applied to an object of class "NULL"
thanks for posting this!
this happened because we made a change in the API and I think the docs you were looking at were out of sync. they should be up to date now. see http://tidytransit.r-transit.org/articles/introduction.html
also, we made a change so that the plot() function will work as specified in the old docs and in the new docs.
Related
I am trying to plot a small rectangle of a map:
library(OpenStreetMap)
upper_left <- c(47.413, 8.551);
lower_right <- c(47.417, 8.556);
map_osm <- openmap(upper_left, lower_right, type = 'osm' );
plot(map_osm );
When I run that, the openmap function gives me the error Error in osmtile(x%%nX, y, zoom, type) : could not obtain tile: 540 298 10.
The documentation of OpenStreetMap seems to indicate that I need to add an API key. However, I am not sure how exactly I would do that (because I use type='osm', not type = url) and I am also unclear where I'd get such an API key from.
The java.lang.NullPointerException and the following R-error (Error in osmtile(...)) seem to come from an older version of OpenStreetMap.
By updating OpenStreetMap to the latest version (0.3.4 currently), the error disappears and the example code of OP should work as it is, without needing an API key.
The accepted answer is not adequate as the error can occur even with the most recent package version.
Sometimes if a particular area is not available in a specific style, you get an error similar to the one mentioned above independent of the package version. The solution would be to try the function with a different style. This is mentioned in the following blog post
As an example, the following modification may solve the issue:
library(OpenStreetMap)
upper_left <- c(47.413, 8.551);
lower_right <- c(47.417, 8.556);
map_osm <- openmap(upper_left, lower_right, type = 'opencyclemap');
plot(map_osm)
I posted this on Bioconductor's support page but didn't any answers hence trying here.
I am using the IdeogramTrack function of R/Biocondutor package, Gviz, from my institution's cluster:
IdeogramTrack(genome="mm10",chromosome="chr1")
When I try this from the master node it works fine but when I try this from any other node in the cluster which IO's through the master node, it hangs and eventually I get the error message:
Error: Internal Server Error
I am able to access enter link description here or any other UCSC mirror through these nodes (using traceroute http://genome.ucsc.edu), and can successfully download data from other repositories such as Ensembl, (e.g., using getBM).
Any idea what's wrong?
BTW, any idea which port is IdeogramTrack trying to use?
it sounds like your institution's cluster has issue fetching annotation data from UCSC through Gviz. One suggestion I have is to see if you can manually download mm9 annotation from UCSC; here is a good place to start, by chromosome. Alternatively, you may use a Bioconductor annotation package such as this.
When you have your data.frame with chromosome and chromosomal information (e.g. mapInfo), you could take advantage of GenomicRanges::makeGRangesFromDataFrame to convert the mm9 annotation to a GRanges object, which allows you to make your own IdeogramTrack object. Details on how to make custom IdeogramTrack can be found here.
In general, here is the workflow:
library(GenomicRanges)
library(Gviz)
mm9_annot <- read.table(<file or url with annotation>)
mm9_granges <- makeGRangesFromDataFrame(mm9_annot)
# Alternatively, you may use rtracklayer package
# mm9_granges <- rtracklayer::import(<file or url with annotation>)
my_ideo <- IdeogramTrack(genome="mm9_custom", bands=mm9_granges)
Hope this helps.
I have downloaded abstracts of interest from pubmed.com then read them using pubmed.mineR package with readabs() function. which is supposed to create object of class "Abstracs", but when I type in ls(), it gives me character(0).
I want to search abstracts using searchabsL(Object,include="protein"),though i don't know how?
mystery solved x = readabs("downloaded file")
thanks Dr.Ramachandran for providing the answer.
I am trying to use the package paleotree to build LTT plots, but I get the following error when I try to input my trees.
a=read.tree(file.choose()) # to choose newick/nexus file
multiDiv(a)
Error in multiDiv(a) : Data of Unknown Type
Does paleotools only take objects of class 'multiphylo' ? I converted the imput tree to class multiphylo, but it still gives the same error. Can anyone suggest how to go about it?
I'm the author of package paleotree. I think what is going on here is that you are passing a single tree to multiDiv, which is setup for analyzing lists of objects, each of which are converted to a diversity curve. You probably want phyloDiv() instead. I can't be certain without know more about your data.
When I want to create the map using the gvisGeoMap() from googleVis, I get error:
## Using the google visualization API with R
library(googleVis)
input<- read.csv("data.csv")
select<- input[which(input$Subgroup=="Total 5-14"),]
select<- input[which(input$Subgroup=="Total 5-14 yr"),]
Map<- data.frame(select$Country.or.Area, select$Value)
names(Map)<- c("Country", "Percentage")
Geo=gvisGeoMap(Map, locationvar="Country", numvar="Percentage",
options=list(height=350, dataMode='regions'))
plot(Geo)
#starting httpd help server ... done
#Error in ifelse(interactive(), getOption("browser"), "false") :
#replacement has length zero
The above is the error in the "RGui". The error message in "RStudio" is differet:
#object of type 'closure' is not subsettable
and the browser does not fire at all. The HTTP server works fine since I can simply call help pages.( for example ?googleVis will fire up the browser and give the help page). The "Geo" object in the code above is fine and contains the html code only that the plot() does not do what it is supposed to do (I can manually run the html file in the temp folder and see the results). The example above is available here.
I would appreciate your clues.
Thank you
This is the result of correspondance with the the Authors of the packages. It seems that there was a bug that prevented the plot to work properly. The released a new version. You can find the link below.
TQ
.....
Yesterday evening I realised that with version 0.3.0 of googleVis I unfortunately introduced a bug in RStudio and R on Windows.
The bug has been fixed already and a new version (0.3.1) is available from our project site (here is the link), but not on CRAN yet.
I have put a note on my blog (here is the link) to inform others as well.
I hope this helps.
Best regards
Markus