I have a loop that executes the body about 200 times. In each loop iteration, it does a sophisticated calculation, and then as debugging, I wish to produce a heatmap of a NxM matrix. But, generating this heatmap is unbearably slow and significantly slow downs an already slow algorithm. My code is along the lines: import numpy import ma...
how can I do a hierarchical clustering (in this case for gene expression data) in Python in a way that shows the matrix of gene expression values along with the dendrogram? What I mean is like the example here: http://www.mathworks.cn/access/helpdesk/help/toolbox/bioinfo/ug/a1060813239b1.html shown after bullet point 6 (Figure 1), whe...
Hi all, Matplotlib and pylab doesn't work in python cgi. but it's working properly in python shell.. Any one can help me....... Plz....... Thanks in advance...... #!C:/Python26/python import cgi import cgitb import sys import os cgitb.enable() # set HOME environment variable to a directory the httpd server can write to os.environ[ 'H...
How can I plot a dendrogram right on top of a matrix of values, reordered appropriately to reflect the clustering, in Python? An example is in the bottom of the following figure: http://www.coriell.org/images/microarray.gif I use scipy.cluster.dendrogram to make my dendrogram and perform hierarchical clustering on a matrix of data. H...
I'm using Matplotlib to dynamically generate .png charts from a database. The user may set as the x-axis any given range of datetimes, and I need to account for all of it. While Matplotlib has the dates.AutoDateLocator(), I want the datetime format printed on the chart to be context-specific - e.g. if the user is charting from 3 p.m. to ...
I have a large graph that I am generating in matplotlib. I'd like to add a number of icons to this graph at certain (x,y) coordinates. I am wondering if there is any way to do that in matplotlib Thank you ...
Hi everybody I have two questions regarding python libraries: I would like to know if there is something like a "super" python library which lets me install ALL or at least all scientific useful python libraries, which I can install once and then I have all I need. There is a number of annoying problems when installing different libra...
I have some surface data that is generated by an external program as XYZ values. I want to create the following graphs, using matplotlib: Surface plot Contour plot Contour plot overlayed with a surface plot I have looked at several examples for plotting surfaces and contours in matplotlib - however, the Z values seems to be a functio...
Can anyone recommend a good matplot tutorial. I am a complete beginner - but have used similar software (matlab, R etc), in my halcyon days at University (i.e. a long time ago). A google search brings up a list of dubious quality, and the 'official' docs are too terse, or provide examples that are more 'edge case' (e.g. drawing dolphins...
Hi probably quite a simple question but.. When plotting a graph using matplotlib.pyplot my Y axis goes from -0.04 to 0.03 which is fine but there are 8 labels for increments (eg 0.03,0.02,0.01 etc.). I need more maybe 16 or so. Thanks for your help ...
I have a series of lines that each need to be plotted with a separate colour. Each line is actually made up of several data sets (positive, negative regions etc.) and so I'd like to be able to create a generator that will feed one colour at a time across a spectrum, for example the gist_rainbow map shown here. I have found the following...
Say I have a list of datetimes, and we know each datetime to be the recorded time of an event happening. Is it possible in matplotlib to graph the frequency of this event occuring over time, showing this data in a cumulative graph (so that each point is greater or equal to all of the points that went before it), without preprocessing th...
I'd like to plot a 2-d matrix from numpy as a colored matrix in Matplotlib. I have the following 9-by-9 array: my_array = diag(ones(9)) # plot the array pcolor(my_array) I'd like to set the first three elements of the diagonal to be a certain color, the next three to be a different color, and the last three a different color. I'd l...
I am using pcolor with a custom color map to plot a matrix of values. I set my color map so that low values are white and high values are red, as shown below. All of my matrices have values between 0 and 20 (inclusive) and I'd like 20 to always be pure red and 0 to always be pure white, even if the matrix has values that don't span the...
I am plotting a simple pair of subplots in matplotlib that are for some reason unevenly centered. I plot them as follows: plt.figure() # first subplot s1 = plt.subplot(2, 1, 1) plt.bar([1, 2, 3], [4, 5, 6]) # second subplot s2 = plt.subplot(2, 1, 2) plt.pcolor(rand(5,5)) # add colorbar plt.colorbar() # square axes axes_square(s1) axes...
I installed matplotlib using the Mac disk image installer for MacOS 10.5 and Python 2.5. I installed numpy then tried to import matplotlib but got this error: ImportError: numpy 1.1 or later is required; you have 2.0.0.dev8462. It seems to that version 2.0.0.dev8462 would be later than version 1.1 but I am guessing that matplotlib got co...
How can I draw only half of a matrix, e.g. the upper / lower part of a matrix, with pcolor for example? Suppose I have a n x n matrix and I draw it using pcolor(my_matrix). I want only the lower half to be shown since other values are redundant. How can this be done? thanks. ...
Hi guys I'm using matplotlib at the moment to try and visualise some data I am working on. I'm trying to plot around 6500 points and the line y = x on the same graph but am having some trouble in doing so. I can only seem to get the points to render and not the line itself. I know matplotlib doesn't plot equations as such rather just a ...
I will have a set of data (x, y, heading), and I need to animate it in real-time. I am currently using matplotlib to animate (x, y) and it works fine, but I would really like to have some way to indicate heading, ie what direction the object is facing. What would be the best library for this? It seems like PyGame might be able to help me...
Hi All I am drawing a plot using matplotlib and pyhon like the sample code below. x = array([0,1,2,3]) y = array([20,21,22,23]) plot(x,y) show() As it is the code above on the x axis I will see drawn values 0.0, 0.5, 1.0, 1.5 i.e. the same values of my reference x values. Is there anyway to map each point of x to a different string...