Question: Python Help: Plots are not appearing in the Spyder Console
gravatar for Wox
5 months ago by
Wox310 wrote:

I am going to analyze proteomics data in Python/Spyder. I did run below scripts in Jupyter and it did work fine. Why don't plots appear in the spyder console? Do these libraries only specific to Jupyter? What should I have to follow to get the scripts in Spyder


structure(list(Protein = structure(3:1, .Label = c("AOX", "Ppt", 
"Sdx"), class = "factor"), Peptide = structure(c(2L, 1L, 3L), .Label = c("EIEYPGQVLR", 
"GLAEFQQK", "TNTDFLPYNGDGFK"), class = "factor"), location = structure(c(2L, 
3L, 1L), .Label = c("Golgi", "Mito", "PEX"), class = "factor"), 
    WT_0t_1 = c(5204L, 5151L, 1135L), WT_0t_2 = c(2794L, 4256L, 
    656L), WT_0t_3 = c(1981L, 3270L, 449L), WT_1t_1 = c(4202L, 
    71366L, 9121L), WT_1t_2 = c(2382L, 44102L, 5389L), WT_1t_3 = c(2190L, 
    55854L, 6719L), WT_3t_1 = c(2060L, 51214L, 9330L), WT_3t_2 = c(2227L, 
    52466L, 9325L), WT_3t_3 = c(1829L, 85549L, 10915L), WT_5t_1 = c(1803L, 
    32629L, 7034L), WT_5t_2 = c(1683L, 38552L, 7947L), WT_5t_3 = c(2501L, 
    83839L, 10031L), wus2_0t_1 = c(4199L, 1604L, 1L), wus2_0t_2 = c(5443L, 
    5550L, 831L), wus2_0t_3 = c(5493L, 4509L, 870L), wus2_1t_1 = c(4540L, 
    18298L, 2863L), wus2_1t_2 = c(3105L, 9892L, 1660L), wus2_1t_3 = c(3801L, 
    15808L, 2550L), wus2_3t_1 = c(2822L, 51167L, 5752L), wus2_3t_2 = c(2286L, 
    26685L, 4859L), wus2_3t_3 = c(2596L, 25978L, 4894L), wus2_5t_1 = c(2058L, 
    22977L, 2619L), wus2_5t_2 = c(2068L, 20512L, 2681L), wus2_5t_3 = c(2309L, 
    27932L, 5662L), wus5_0t_1 = c(4573L, 2731L, 254L), wus5_0t_2 = c(6558L, 
    3924L, 0L), wus5_0t_3 = c(6618L, 4635L, 861L), wus5_1t_1 = c(6235L, 
    30751L, 4703L), wus5_1t_2 = c(2866L, 14198L, 2944L), wus5_1t_3 = c(4997L, 
    22038L, 3930L), wus5_3t_1 = c(2939L, 26945L, 4571L), wus5_3t_2 = c(4872L, 
    41267L, 4442L), wus5_3t_3 = c(4129L, 36632L, 6963L), wus5_5t_1 = c(3966L, 
    58892L, 10088L), wus5_5t_2 = c(2933L, 77223L, 7056L), wus5_5t_3 = c(2799L, 
    42703L, 8511L), wus7_0t_1 = c(4202L, 6298L, 311L), wus7_0t_2 = c(1871L, 
    3735L, 413L), wus7_0t_3 = c(2076L, 2092L, 193L), wus7_1t_1 = c(3492L, 
    19426L, 1586L), wus7_1t_2 = c(2659L, 18379L, 3616L), wus7_1t_3 = c(3097L, 
    22991L, 1806L), wus7_3t_1 = c(839L, 26725L, 4855L), wus7_3t_2 = c(3309L, 
    68651L, 7717L), wus7_3t_3 = c(2215L, 28616L, 4207L), wus7_5t_1 = c(776L, 
    26765L, 6191L), wus7_5t_2 = c(2460L, 105244L, 9085L), wus7_5t_3 = c(2431L, 
    97977L, 10984L), wus9_0t_1 = c(3152L, 4976L, 682L), wus9_0t_2 = c(3253L, 
    3826L, 0L), wus9_0t_3 = c(2818L, 5648L, 423L), wus9_1t_1 = c(1024L, 
    11057L, 2741L), wus9_1t_2 = c(2093L, 17916L, 1855L), wus9_1t_3 = c(1743L, 
    13561L, 2047L), wus9_3t_1 = c(2406L, 46471L, 6354L), wus9_3t_2 = c(1709L, 
    41807L, 4243L), wus9_3t_3 = c(2490L, 59844L, 6709L), wus9_5t_1 = c(2084L, 
    50857L, 8948L), wus9_5t_2 = c(1217L, 33163L, 6777L), wus9_5t_3 = c(1173L, 
    102291L, 13028L)), class = "data.frame", row.names = c(NA, 

I have used below scripts for plotting, which perfectly work in Jupyter.

df.loc[df.location == 'Cytolsol_ribo', 'location'] = 'Cytosol_ribo'
df = df[df.location != 'Median']

df2 = df2.set_index(['location'])

df2 = df2.stack().to_frame()

df2 = df2.reset_index()

df2.columns = ['location', 'exp', 'val']
df2['mutant'], df2['time'], df2['replicate'] = df2.exp.str.split('_').str

df2 = df2.drop('exp', axis=1)
df2 = df2[['location', 'mutant', 'time', 'replicate', 'val']]

box_opts = opts.BoxWhisker(height=400,

g = y='val', by=['mutant', 'time'], groupby='location')


I do not get the plots in the Spyder console. What may be the reason?

omics python • 682 views
ADD COMMENTlink written 5 months ago by Wox310

I am not familiar with Spyder. But if the plotting is done by matplotlib under the hood, I guess you may use to visualize it.

ADD REPLYlink modified 5 months ago • written 5 months ago by shoujun.gu280

Thanks, shoujun. I had a look. it doesn't work, unfortunately.

ADD REPLYlink modified 5 months ago • written 5 months ago by Wox310

looks like hvPlot using Bokeh under the hood. You may try something like:

ADD REPLYlink written 5 months ago by shoujun.gu280

No luck shoujun, dosn't work
Traceback (most recent call last):

  File "<ipython-input-74-49d321d018a1>", line 1, in <module>

NameError: name 'bokeh' is not defined
ADD REPLYlink written 5 months ago by Wox310

have you installed and imported bokeh?

ADD REPLYlink written 5 months ago by shoujun.gu280

Yes, But still I do not see plots appearing in the console

ADD REPLYlink written 5 months ago by Wox310
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