I have created an alluvial plot but, for visibility purposes I would like to move one lode in one of the axes: more specifically I would like the "NA" of the "Type of surgery" to be at the top so the last 4 axes are aligned.
This is the code I used on R:
aes(y = ID, axis1 = Reason, axis2 = Response, axis3=Type_of_surgery, axis4=Margins, axis5=RT_post_op, axis6=Chemo_post_op)) +
geom_alluvium(aes(fill = Type_of_surgery), width = 1/12,aes.bind = TRUE) +
geom_flow(aes.bind = TRUE) +
geom_stratum(width = 1/3, fill = "grey", color = "white") +
geom_label(stat = "stratum", aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Reason", "Response","Type of surgery", "Margins","RT post op", "Chemo post-op"), expand = c(0.1,0.1)) +
scale_fill_brewer(type = "qual", palette = "Pastel1") +
ggtitle("TBC") ```
This is the plot I obtained:
[Alluvial plot][1]
[1]: https://i.stack.imgur.com/nDCIZ.png
I am beginning on the world of coding so any help would be most welcome,
Thank you all for your help,
JB
Related
i am reading the document https://plotly.com/r/reference/sankey/, and want to change the links color for a sankey chart. But i can't quite understand the parameters in add_trace() function
where should i specify the color value?
add_trace(p,type='sankey', color=????)
You haven't provided a minimal reproducible example, so I can't jump right into your code. But I think I can point you in the right direction.
In the documentation you screenshotted, it's saying that the color argument is one key of the list link that defines links in the plot. Using this example from the R plotly documentation for adding links, let's take a look at where that goes:
library(plotly)
library(rjson)
json_file <- "https://raw.githubusercontent.com/plotly/plotly.js/master/test/image/mocks/sankey_energy.json"
json_data <- fromJSON(paste(readLines(json_file), collapse=""))
fig <- plot_ly(
type = "sankey",
domain = list(
x = c(0,1),
y = c(0,1)
),
orientation = "h",
valueformat = ".0f",
valuesuffix = "TWh",
node = list(
label = json_data$data[[1]]$node$label,
color = json_data$data[[1]]$node$color,
pad = 15,
thickness = 15,
line = list(
color = "black",
width = 0.5
)
),
link = list(
source = json_data$data[[1]]$link$source,
target = json_data$data[[1]]$link$target,
value = json_data$data[[1]]$link$value,
label = json_data$data[[1]]$link$label,
#### Color goes here! ####
color = "yellow"
)
)
fig <- fig %>% layout(
title = "Energy forecast for 2050<br>Source: Department of Energy & Climate Change, Tom Counsell via <a href='https://bost.ocks.org/mike/sankey/'>Mike Bostock</a>",
font = list(
size = 10
),
xaxis = list(showgrid = F, zeroline = F),
yaxis = list(showgrid = F, zeroline = F)
)
fig
The plotly documentation can be a bit opaque at times. I have found it helpful to sometimes review the documentation for python. For example, this part of the python documentation does give some more guidance about changing link colors.
When I try to draw a map with a Hobo–Dyer projection, it told me:
Error in st_crs.character(x[[shape.id[masterID]]]$projection) : invalid crs: hd
Here is my code:
tm_shape(countries_spdf, projection = "hd") +
tm_grid(n.x = 11, n.y = 11) +
tm_fill(col = "population", style = "quantile") +
tm_borders(col = "burlywood4")
What should I do?
I believe the projection feature of tm_shape has been changed to only take on integers representing the desired CRS. i.e. it still works with 4326, which is the most common one in the industry. However there is workaround using coord_map from ggplot library which I have included below:
tm_shape(countries_spdf, projection = 4326) +
tm_grid(n.x = 11, n.y = 11) +
tm_fill(col = "population", style = "quantile") +
tm_borders(col = "burlywood4")
tm_shape(countries_spdf, projection = coord_map("hr")) +
tm_grid(n.x = 11, n.y = 11) +
tm_fill(col = "population", style = "quantile") +
tm_borders(col = "burlywood4")
Hope this helps
I have a set of images in a folder which their names are: 2 days.bmp 3 days.bmp ..... 28 days.bmp. Also, I have a folder with the background images exactly with the same names. I want to use the calculator plus and divide each image to its relevant background. I want to save time and do that at the same time instead of doing it for each image one by one. Is there any idea how can I do that? I have written a macro but it didn't work for me.
macro "Batch calculate images [1]" {
LocationOfFiles = getDirectory("Select Folder");
LocationOfbackgrounds = getDirectory("Select Folder of backgrounds");
LocationOfSave = getDirectory("Select Save Location");
setBatchMode(true);
FileList = getFileList(LocationOfFiles);
NumberOfFiles = FileList.length;
for (i=0; i<NumberOfFiles; i+=1) {
FileName = FileList[i];
pathtofile1 = LocationOfFiles+FileName;
open(pathtofile1);
name1 = getTitle();
pathtofile2 = LocationOfbackgrounds+FileName;
open(pathtofile2);
name2 = getTitle();
run("Calculator Plus", "i1="+name1+" i2="+name2+" operation=[Divide: i2 = (i1/i2) x k1 + k2] k1=255 k2=0 create");
selectWindow("Result");
SaveName = replace(name, ".bmp", "_backgroud subtracted.jpg");
saveAs("BMP", LocationOfSave+SaveName);
selectWindow(BackgroundImage);
close("\\Others");
I am quite new to Matlab and I am trying to use this code I found online.
I am trying to fit a graph described by the HydrodynamicSpectrum. But instead of having it fit after inputting fvA and fmA, I am trying to obtain the fitted parameters for this value also.
I have tried removing them, changing them. But none is working. I was wondering if any one here will be able to point me into the right direction of fixing this.
specFunc = #(f, para)HydrodynamicSpectrum(f, [para fvA fmA]);
[fit.AXfc, fit.AXD] = NonLinearFit(fit.f(indXY), fit.AXSpec(indXY), specFunc, [iguess_AXfc iguess_AXD]);
[fit.AYfc, fit.AYD] = NonLinearFit(fit.f(indXY), fit.AYSpec(indXY), specFunc, [iguess_AYfc iguess_AYD]);
[fit.ASumfc, fit.ASumD] = NonLinearFit(fit.f(indSum), fit.ASumSpec(indSum), specFunc, [iguess_ASumfc iguess_ASumD]);
predictedAX = HydrodynamicSpectrum(fit.f, [fit.AXfc fit.AXD fvA fmA]);
predictedAY = HydrodynamicSpectrum(fit.f, [fit.AYfc fit.AYD fvA fmA]);
predictedASum = HydrodynamicSpectrum(fit.f, [fit.ASumfc fit.ASumD fvA fmA]);
function spec = HydrodynamicSpectrum(f, para);
fc = para(1);
D = para(2);
fv = para(3);
fm = para(4);
f = abs(f); %Kludge!
spec = D/pi^2*(1+sqrt(f/fv))./((fc - f.*sqrt(f./fv) - (f.^2)/fm).^2 + (f + f.*sqrt(f./fv)).^2);
function [fc, D, sfc, sD] = NonLinearFit(f, spec, specFunc, init);
func = #(para, f)spec./specFunc(f, para);
[paraFit, resid, J] = nlinfit(f, ones(1, length(spec)), func, init);
fc = paraFit(1);
D = paraFit(2);
ci = nlparci(real(paraFit), real(resid), real(J)); % Kludge!!
sfc = (ci(1,2) - ci(1,1))/4;
sD = (ci(2,2) - ci(2,1))/4;
[paraFit, resid, J] = nlinfit(f, ones(1, length(spec)), func, init);
It looks like you get your fitted parameter using this line. And you are further processing them to get other stuff out from the function. You can modify your second function to get them out as well.
As there are very few comments, and questions seems to be application specific, there is not much help I can give with what you have presented.
I have a weird problem... I can't make legend: Lets say I have:
fraction1Str = strcat('F1 = ', sprintf('%g',round(fraction1*100)/100), '+/-',sprintf('%g',round(fraction1STD*100)/100));
fraction2Str = strcat('F2 = ', sprintf('%g',round(fraction2*100)/100), '+/-',sprintf('%g',round(fraction2STD*100)/100));
fraction3Str = strcat('F3 = ', sprintf('%g',round(fraction3*100)/100), '+/-',sprintf('%g',round(fraction3STD*100)/100));
fractionStr = [fraction1Str; fraction2Str; fraction3Str];
...
hleg = legend(fractionStr);
That is giving me error: CAT arguments dimensions are not consistent.
All strings are the same format, even number of chars... Interestingly if I change to one of i.e.
fractionStr = [fraction3Str; fraction3Str; fraction3Str];
fractionStr = [fraction2Str; fraction2Str; fraction2Str];
fractionStr = [fraction1Str; fraction1Str; fraction1Str];
its working, but no with these three different strings... Any ideas?