How do I set up the color for NaN in holoviews.points? Especially given that I am sampling the dataset with .where. Applying clipping colors gives the following error:
Unexpected option 'clipping_colors' for Overlay type across all extensions. No similar options found. It is not a background color either.
The code to generate my plot (bear in mind it is an xarray Dataset):
ds_30_365.beta.sel(pc=1).where(ds_30_365.pval.sel(pc=1)<0.2).hvplot.points(c='beta',coastline = True, cmap ='RdBu_r',clim=(-0.025,0.025)).opts(width=600,padding=(0,0))
The whole thing is an example of stippling and ideally I'd like to see ocean part being grey and the land remaining white. There is no data in the land part but everything ends up grey.
Thank you!
Related
As mentioned in the question, is there anyway we can change color of bar and waterfall plot in shap plot? I didn't see any option to change it. I tried using matplotlib to change the color but that didn't solve the issue. I can add the title but can't change the color. Any help would be great.
plt.title("This is my title")
plt.gray()
shap.plots.bar(shap_values,show = False)
shap.plots.waterfall(shap_values[-1])
plt.show()
Thanks,
Sam
I had a similar issue. I wanted to swap the blue color with the red one in the shap waterfall plot.
My approach was modifying the file _waterfall.py in the shap lib, replacing the lines with c = colors.red_rgb with c = colors.blue_rgb and vice-versa.
Surely not an elegant solution but I just needed to generate 6 plots this way.
I am trying to create multiple graphs that share the same legend.
I have found many ways to combine multiple graphs and it seems that ggarrange has the ability to create one shared legend for all that is supposed to be unique.
However I am having some problems when graphing since a few of the graphs do not have the same phyla (what defines the legend colors) present, but I would like them all to be the same colors throughout all of the graphs so the combined legend will have the correct colors.
For just one graph I would assign a color to the label manually like below
labs<-c("Arthropoda"="#FF66CC"
,"Cercozoa"="#FF6000")
and plot with the addition of scale_fill_manual(values=labs) and this seems to work
then I modified it so I could have portions of them italicized.
labsPhylum <-c('expression(paste(italic("Arthropoda")))'="#CC0000"
,'expression(paste(italic("Cercozoa")))'= "#FF6000"
,'expression (paste("unknown", ~italic("Eukaryota")))'= "#990000")`
However when I create a plot using ggplot and scale_color_manual() using the labsPhylum that I think should be italicized and colored I plot an empty graph with this warning so there is something vital I am not understanding here.
ggplot(data=sigtab_dil, aes(x=Species, y=log2FoldChange, color=Phylum))+
geom_point(size=2) +
scale_color_manual(values=labsPhylum)
Warning message:
Removed 9 rows containing missing values (geom_point).
Could someone please help me figure out where I am going wrong?
Thank you
Answered my own question
I realized I had to make separate vectors for breaks, labels, and values rather than combining them.
In short
colsPhylum <-c("Arthropoda"="#CC0000"
,"Cercozoa"= "#FF6000"
,"Chlorophyta"= "#CC9900"
labsPhylum <-c(expression(paste(italic("Arthropoda")))
,expression(paste(italic("Cercozoa")))
,expression(paste(italic("Chlorophyta ")))
breaksPhylum <-c("Arthropoda", "Cercozoa","Chlorophyta", "Choanozoa"
,"Ciliophora"
,"Cryptista"
I am processing an image with OpenCV on Python and I want to count every objects (worms) on it. Worms are rather light beige whereas the background is black (see picture) so it is rather easy to distinguish them. The problem is that sometimes worms are too close to each other (sometimes they even overlap) and cv.findContours() will draw one big contour instead of two smaller ones (see picture below).
Because I am using cv.foundContours(), I have to first turn the picture into black and white, then blur it (optional) and finally threshold it in order to have white worms in a black background.
I am using the following code :
import cv2 as cv
img = cv.imread('worms.jpg')
gray = cv.cvtColor(img, cv.COLOR_BGR2GRAY)
blur=cv.GaussianBlur(gray,(5,5),1)
ret,osu = cv.threshold(blur,0,255,cv.THRESH_BINARY+cv.THRESH_OTSU)
imsource,contours,test = cv.findContours(osu,1,1)
cv.drawContours(img,contours,-1, (0,0,255),2)
I tried to erode the thresholded picture but it doesn't work well since the "bond" between two worms is quite big.
Thanks for the help
Using gnuplot v5 patch 6 on windows 10 (wxt terminal)
I have a data file of 2D vectors arranged in six columns (x, y, v_x, v_y, v_mag, rho) that I'm trying to plot as a heatmap of v_mag against x and y. The plot generates fine, but it's always coming up with
"No dimension information for 80000 pixels total. Try 200 x 400"
But I have no idea where to specify this in the terminal.
I realise that I can use pm3d map for this, but this doesn't work without setting dgrid3d and that causes problems with plotting dots on top of the heatmap which I'm also doing. I also don't want to generate a matrix file just for the image plot since I need the vector data for analysis later.
In terms of an example, the plot will generate if I literally just write:
plot 'vectors.dat' using 1:2:5 with image, 'dots.dat' with dots
EDIT: added 'set pm3d' to example code
EDIT: example is now minimal code to produce desired plot
EDIT: example data file can be found here
Any help would be appreciated.
After updating my gnuplot to v5.2, this problem has disappeared.
I want to not have my basemap axes visible for an image I'm making in GMT with several plots in it. So far I have made them white using:
gmtset BASEMAP_FRAME_RGB = white
However some of the plots partially overlap and the white axes can be seen over the plots - any ideas on how to fix this? By making the basemap frame transparent ideally.
In fact I've realised I can change the order I do the plots in so that the overlap doesn't matter - also replaced -B... with -G255 to plot on a blank square.