Time series from Dataframe: Plotting X-values from rows and Y-values from Column Values

Question

I'm trying to create a line plot (time series) from a filtered data frame that is 17 rows x 33 columns.

To provide some background, I am tracking gene expression over certain time points. Every row in this data frame corresponds to a particular exon. Every column on this data frame corresponds to a time-point, while the VALUES INSIDE the columns correspond to level of gene expression.

This is what my data frame looks like:

I want to create a line graph where every line corresponds to a row on this data frame (exon), while the y-values correspond to level of gene expression (values inside each column).

I'm trying to get a resulting graph that would something like this:

Is there anyway to do this? I've tried to set the x and y axes individually but I think the error might stem from using labels and integer-values interchangeably. This is the method I tried using:

df2.plot(x=df2['0'], y=df2['38', '56', '65', '79', '99', '110', '128', '138', 
                       '146', '171', '183', '198', '206', '218', '231', '238', 
                       '258', '276', '283', '303', '316', '331', '343', '367', 
                       '379', '383', '412', '430', '438', '471', '484', '496', '521'])

But this produces this instead:

Any help would be greatly appreciated.

Barracudovich · Accepted Answer · 2023-02-02 17:02:16Z

1

If I got the problem correctly, transpose should help here:

P.S. It was randomly generated data

UPDATE:

Will reflect comment here for the sake of consistency. Seems like the column name is a string in your case, here is how it should work in that case

edited Feb 2, 2023 at 17:02

answered Feb 2, 2023 at 4:44

Barracudovich

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3 Comments

Marstian Over a year ago

Thanks for the reply, that definitely looks like what I'm trying to achieve! Unfortunately I tried using this method but got "KeyError: None of [0] are in the columns." I think the issue may be that the first column is named "0" ? Not sure how I would change that though.

Barracudovich Over a year ago

Good. In my case the column name was integer. Looks like this option should work for you: df.set_index("0")

Marstian Over a year ago

Thanks for the help. I've discovered that the first column is actually an index, which is why it's so finicky with the code. I have changed the name of the index by using df2.index.name = 'exon' and then ran your code. It works thanks!

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