I have an Xarray Dataset which looks like
I would like to be able to select data variables (which i already know how to do) and plot a quadmesh of the data variable selected. The problem is that different data variables have different numbers and types of coordinates which means the closest I got is having a really long hard coded switch statement to handle each possible data variable and have a sel on it with the appropriate number and type of coordinates (for ES I would need to select on pres1 and time). How would I approach this in order to be able to allow the user to visualize the geospatial data no matter the data variable selected?
Here is my current attempt :
select_field = pnw.Select(name="Field", options=list(xds.data_vars))
select_time = pnw.Select(name="Time", options=list(xds.coords['time'].values))
select_pres1 = pnw.Select(name="Pressure 1", options=list(xds.coords['pres1'].values))
def fieldFiltered(select_field):
return xds[select_field]
xdsi = hvplot.bind(fieldFiltered, select_field).interactive(sizing_mode='stretch_both')
wid = xdsi.sel( pres1=select_pres1 , time=select_time ).widgets()
ploti = xdsi.sel(time=select_time).hvplot()
pn.Row(
wid[1],
wid[2],
ploti
)
which gives me something similar to
but breaks for any other variable
Related
I'm trying to extract the data matrix computed by Signac r package when running RegionMatrix(). I know I can plot the data with RegionHeatmap(), but I want to plot the data with another package.
So, if I created a region matrix like this:
my_object <- RegionMatrix(my_object
, key = "my_region_matrix"
, regions = StringToGRanges(top_cluster_genes$gene)
, upstream = 2500, downstream = 2500)
How do I go about extracting the data stored within the object under the key "my_region_matrix"? I know it's a pretty basic question, but I've been browsing the returned object and can't find any assay/matrix with that key name. (I'm putting this under Seurat because apparently there is no tag for Signac and the object is a Seurat object anyway)
There are R native datasets, such as the Nile dataset, that are time series. However, if I actually look at the data set, be it as it was, after as_tibble(), after as.data.frame() – it doesn't matter –, there is only one column: x (which, in this specific case, is the "measurement of anual flow of the river"). However, if I plot() the data, in any of the three formats (raw, tibble or data.frame), I plots with the dates:
(Technically, the x axis label changes, but that's not the point).
Where are these dates stored? How can I access them (to use ggplot(), for example), or even – how can I see them?
If you use str(Nile) or print(Nile), you'll see that the Nile data set is store in a Time-Series object. You can use the start(), end() and frequency() functions to extract those attribute then create a new column to store those informations.
data(Nile)
new_df = data.frame(Nile)
new_df$Time = seq(from = start(Nile)[[1]], to = end(Nile)[[1]], by = frequency(Nile))
I am kind of new to using RStudio...I love analyzing data by viewing it in separate window or tab inside the IDE..I am using RStudio to read specific columns from a dataset....I want to open the value stored in a variable in a separate window or tab...The variable contain only one column...Like for example i want to open the values of Y in a separate Window or Tab just like X...How can i do it?
Here is the complete code i am using
dataset<-read.csv('C:\\Users\\datasets\\landprice1.csv')
X = dataset[ 1:14, (1:3)]
Y = dataset[ 1:14,(4)]
Note : The variable Y contain one one column have several observations while X contain 3 columns have several observations. Also i searched a lot on Google before coming here but could find my answer
If you want to open a matrix or a data frame or what else you can just use View() function.
dataset<-read.csv('C:\\Users\\datasets\\landprice1.csv')
X = dataset[ 1:14, (1:3)]
Y = dataset[ 1:14,(4)]
View(X)
View(Y)
I have a data frame that I am trying to condense from multiples rows into one row.The data set is fairly large, but I am starting with a small subset. So here I want to turn 2 rows into 1; I want the information to follow the information in the first row.
The original problem was that I had a column of data that I need to "flatten" so that I can use the bits and pieces. The column is in JSON format.
"[{\"task\":\"T0\",\"task_label\":\"Did any birds visit the feeding platform or bird feeders?\",\"value\":\"**Yes**—but there were no displacements. Next, enter all of the birds you see at the feeders. \"},{\"task\":\"T1\",\"value\":[{\"choice\":\"EUROPEANSTARLING\",\"answers\":{\"WHATISTHELARGESTNUMBEROFINDIVIDUALSTHATYOUSAWSIMULTANEOUSLY\":\"4\"},\"filters\":{}},{\"choice\":\"MOURNINGDOVE\",\"answers\":{\"WHATISTHELARGESTNUMBEROFINDIVIDUALSTHATYOUSAWSIMULTANEOUSLY\":\"2\"},\"filters\":{}}]},{\"task\":\"T6\",\"task_label\":\"Is it actively precipitating (rain or snow)?\",\"value\":[\"Yes.\"]}]"
So I used code developed by another coder to "flatten" this out by task. Then, I want to join it back up so that I have one line of information for each classification.
Currently, I have merged tasks T0 and T4, but I need to merge this to another task, T5. In order to do that, I need to reduce the data in merge of T0 and T4 to one row. So right now I'm working with a small subset of the data and have a table that essentially looks like this:
x <- data.frame("subject_ids" = c(19232716, 19232716), "classification_id" = c(120545061,120545061), "task_index.x" = c(1,1),
"task.x" = c("TO","TO"), "value" = c("Displacement","Displacement"), "task_index.y"=c(2,5), "task.y"= c("T4, T4","T4"),
"total.species"=c("2,2","1"), "choice" = c("MOURNINGDOVE, COMMONGRACKLE","MOURNINGDOVE"), "S_T"=c("Target,Target","Target,Source"))
but I want it to look like this:
y <- data.frame("subject_ids" = c(19232716), "classification_id" = c(120545061), "task_index.x" = c(1),
"task.x" = c("TO"), "value" = c("Displacement"), "task_index.y"=c(2), "task.y"= "T4, T4",
"total.species"=c("2,2"), "choice" = c("MOURNINGDOVE, COMMONGRACKLE"), "S_T"=c("Target,Target"),
"task_index.y"=c(5), "task.y"= "T4",
"total.species"=c("1"), "choice" = c("MOURNINGDOVE"), "S_T"=c("Target,Source"))
Using leaflet, I'm trying to plot some lines and set their color based on a 'speed' variable. My data start at an encoded polyline level (i.e. a series of lat/long points, encoded as an alphanumeric string) with a single speed value for each EPL.
I'm able to decode the polylines to get lat/long series of (thanks to Max, here) and I'm able to create segments from those series of points and format them as a SpatialLines object (thanks to Kyle Walker, here).
My problem: I can plot the lines properly using leaflet, but I can't join the SpatialLines object to the base data to create a SpatialLinesDataFrame, and so I can't code the line color based on the speed var. I suspect the issue is that the IDs I'm assigning SL segments aren't matching to those present in the base df.
The objects I've tried to join, with SpatialLinesDataFrame():
"sl_object", a SpatialLines object with ~140 observations, one for each segment; I'm using Kyle's code, linked above, with one key change - instead of creating an arbitrary iterative ID value for each segment, I'm pulling the associated ID from my base data. (Or at least I'm trying to.) So, I've replaced:
id <- paste0("line", as.character(p))
with
lguy <- data.frame(paths[[p]][1])
id <- unique(lguy[,1])
"speed_object", a df with ~140 observations of a single speed var and row.names set to the same id var that I thought I created in the SL object above. (The number of observations will never exceed but may be smaller than the number of segments in the SL object.)
My joining code:
splndf <- SpatialLinesDataFrame(sl = sl_object, data = speed_object)
And the result:
row.names of data and Lines IDs do not match
Thanks, all. I'm posting this in part because I've seen some similar questions - including some referring specifically to changing the ID output of Kyle's great tool - and haven't been able to find a good answer.
EDIT: Including data samples.
From sl_obj, a single segment:
print(sl_obj)
Slot "ID":
[1] "4763655"
[[151]]
An object of class "Lines"
Slot "Lines":
[[1]]
An object of class "Line"
Slot "coords":
lon lat
1955 -74.05228 40.60397
1956 -74.05021 40.60465
1957 -74.04182 40.60737
1958 -74.03997 40.60795
1959 -74.03919 40.60821
And the corresponding record from speed_obj:
row.names speed
... ...
4763657 44.74
4763655 34.8 # this one matches the ID above
4616250 57.79
... ...
To get rid of this error message, either make the row.names of data and Lines IDs match by preparing sl_object and/or speed_object, or, in case you are certain that they should be matched in the order they appear, use
splndf <- SpatialLinesDataFrame(sl = sl_object, data = speed_object, match.ID = FALSE)
This is documented in ?SpatialLinesDataFrame.
All right, I figured it out. The error wasn't liking the fact that my speed_obj wasn't the same length as my sl_obj, as mentioned here. ("data =
object of class data.frame; the number of rows in data should equal the number of Lines elements in sl)
Resolution: used a quick loop to pull out all of the unique lines IDs, then performed a left join against that list of uniques to create an exhaustive speed_obj (with NAs, which seem to be OK).
ids <- data.frame()
for (i in (1:length(sl_obj))) {
id <- data.frame(sl_obj#lines[[i]]#ID)
ids <- rbind(ids, id)
}
colnames(ids)[1] <- "linkId"
speed_full <- join(ids, speed_obj)
speed_full_short <- data.frame(speed_obj[,c(-1)])
row.names(speed_full_short) <- speed_full$linkId
splndf <- SpatialLinesDataFrame(sl_obj, data = speed_full_short, match.ID = T)
Works fine now!
I may have deciphered the issue.
When I am pulling in my spatial lines data and I check the class it reads as
"Spatial Lines Data Frame" even though I know it's a simple linear shapefile, I'm using readOGR to bring the data in and I believe this is where the conversion is occurring. With that in mind the speed assignment is relatively easy.
sl_object$speed <- speed_object[ match( sl_object$ID , row.names( speed_object ) ) , "speed" ]
This should do the trick, as I'm willing to bet your class(sl_object) is "Spatial Lines Data Frame".
EDIT: I had received the same error as OP, driving me to check class()
I am under the impression that the error that was populated for you is because you were trying to coerce a data frame into a data frame and R wasn't a fan of that.