sashimi_plot_settings

[data]
# directory where BAM files are
bam_prefix = /home/591608/home/591608/misobams/Hacat/unpaired/
# directory where MISO output is
miso_prefix = /home/591608/misoresults/
bam_files = [
    "SRX3643700/SRR6666839.Aligned.sortedByCoord.out.sorted.bam",
    "SRX3643701/SRR6666840.Aligned.sortedByCoord.out.sorted.bam",
    "SRX3643702/SRR6666841.Aligned.sortedByCoord.out.sorted.bam"
      ]

miso_files = [
    "SRX3643700",
    "SRX3643701",
    "SRX3643702"
    ]

[plotting]
# Dimensions of figure to be plotted (in inches)
fig_width = 35
fig_height = 20
# 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 = 10 

bar_posteriors = TRUE

# Max y-axis
ymax = 5

# 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 = FALSE

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

resolution = 1
posterior_bins = 50
gene_posterior_ratio = 8

# List of colors for read denisites of each sample
colors = [
    "#CC0011",
    "#0000ff",
    "#0FBE09"
    ]

# Number of mapped reads in each sample
# (Used to normalize the read density for RPKM calculation)
coverages = [
    544,
    69432,
    53605,
    ]

# 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.