Upon running :

`sashimi_plot --plot-bf-dist sample3_vs_sample3.miso_bf settings.txt --output-dir plots/`

I get the following error:

home/pachecop/pachecop/splicing/BamFiles/myenv/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:106: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid module was deprecated in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead.
      warnings.warn(message, mplDeprecation, stacklevel=1)

Which led me to change the settings in the plotting.py files in

/misopy_original/sashimi_plot/plot_utils and /misopy/sashimi_plot/plot_utils/

and changing the lines:

`from mpl_toolkits.axes_grid import SubplotZero`

`from mpl_toolkits.axisartist import SubplotZero`

In both plotting.py files. When I do this and re-run the code:

`sashimi_plot --plot-bf-dist sample3_vs_sample3.miso_bf settings.txt --output-dir plots/`

I get no error messages, but no plots or /plots folder is created.

My settings file is set up as follows:

```

[data]

directory where BAM files are

bam_prefix = ~/pachecop/splicing/BamFiles
# directory where MISO output is
miso_prefix = ~/pachecop/splicing/BamFiles/comparisons/control_vs_day8/sample3_vs_sample3

bam_files = [
    "BL6NSCD0S-1_ppm.bam",
    "BL6NSCD0S-2_ppm.bam",
    "BL6NSCD0S-3_ppm.bam",
    "BL6NSCD8ConS-1_ppm.bam",
    "BL6NSCD8ConS-2_ppm.bam",
    "BL6NSCD8ConS-3_ppm.bam",]

miso_files = [
    "sample1c",
    "sample2c",
    "sample3c",
    "sample1t",
    "sample2t",
    "sample3t"]

[plotting]
# Dimensions of figure to be plotted (in inches)
fig_width = 7
fig_height = 5
# Factor to scale down introns and exons by
intron_scale = 30
exon_scale = 4
# Whether to use a log scale or not when plotting
logged = False
font_size = 6

bar_posteriors = False

# Max y-axis
ymax = 150

# Axis tick marks
nyticks = 3
nxticks = 4

# Whether to show axis labels
show_ylabel = True
show_xlabel = True

# Whether to plot posterior distributions inferred by MISO
show_posteriors = True

# Whether to plot the number of reads in each junction
number_junctions = True

resolution = .5
posterior_bins = 40
gene_posterior_ratio = 5

# List of colors for read denisites of each sample
colors = [
    "#CC0011",
    "#CC0011",
    "#FF8800",
    "#FF8800"]

# Number of mapped reads in each sample
# (Used to normalize the read density for RPKM calculation)
coverages = [
    6830944,
    14039751,
    4449737,
    6720151]

# Bar color for Bayes factor distribution
# plots (--plot-bf-dist)
# Paint them blue
bar_color = "b"

# Bayes factors thresholds to use for --plot-bf-dist
bf_thresholds = [0, 1, 2, 5, 10, 20]

##
## Names of colors for plotting
##
# "b" for blue
# "k" for black
# "r" for red
# "g" for green
#
# Hex colors are accepted too.

yarden / MISO

Problems with mpl_toolkits.axes_grid #118

directory where BAM files are