could it plot DTU based on many samples with same one condition?

[icanccwhite]

hi, the question should be many samples with same one condition, is that okay?

[kvittingseerup]

Yep. That is automativally handled by all plot functions except the switchPlot 😊

man. 3. apr. 2023 kl. 18.14 skrev Little Fish (Yu) @.***

:

— Reply to this email directly, view it on GitHub https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues/183, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFU7JY4ZTYULIJIJRJV4YO3W7LZOVANCNFSM6AAAAAAWRRIE24 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Cheers Kristoffer

[kvittingseerup]

That should work just fine. In fact that is the preferred data to work with 😊

ons. 12. apr. 2023 kl. 09.31 skrev Little Fish (Yu) < @.***>:

hi, the question should be many samples with same one condition, is that okay?

— Reply to this email directly, view it on GitHub https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues/183#issuecomment-1504800593, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFU7JY4C65ZPOULJLXTFSG3XAZK43ANCNFSM6AAAAAAWRRIE24 . You are receiving this because you commented.Message ID: @.***>

-- Cheers Kristoffer

[rvermamsm]

I ran it with 7 condition and want to plot volcano like plot using below code:

#volcano like plot (q.value_vs_dIF) ggplot(data=intronRetention$isoformFeatures, aes(x=dIF, y=-log10(isoform_switch_q_value))) + geom_point( aes( color=abs(dIF) > 0.1 & isoform_switch_q_value < 0.05 ), # default cutoff size=1 ) + geom_hline(yintercept = -log10(0.05), linetype='dashed') + # default cutoff geom_vline(xintercept = c(-0.1, 0.1), linetype='dashed') + # default cutoff facet_wrap( ~ condition_2) + #facet_grid(condition_1 ~ condition_2) + # alternative to facet_wrap if you have overlapping conditions scale_color_manual('Signficant\nIsoform Switch', values = c('black','red')) + labs(x='dIF', y='-Log10 ( Isoform Switch Q Value )') + theme_bw()

but it generate plot for only 5 condition. Could it plot for more than 5 conditions?

[rvermamsm]

Yep. That is automativally handled by all plot functions except the switchPlot 😊 man. 3. apr. 2023 kl. 18.14 skrev Little Fish (Yu) @.*** : — Reply to this email directly, view it on GitHub <#183>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFU7JY4ZTYULIJIJRJV4YO3W7LZOVANCNFSM6AAAAAAWRRIE24 . You are receiving this because you are subscribed to this thread.Message ID: @.***> -- Cheers Kristoffer

I ran it with 7 condition and want to plot volcano like plot using below code:

#volcano like plot (q.value_vs_dIF) ggplot(data=intronRetention$isoformFeatures, aes(x=dIF, y=-log10(isoform_switch_q_value))) + geom_point( aes( color=abs(dIF) > 0.1 & isoform_switch_q_value < 0.05 ), # default cutoff size=1 ) + geom_hline(yintercept = -log10(0.05), linetype='dashed') + # default cutoff geom_vline(xintercept = c(-0.1, 0.1), linetype='dashed') + # default cutoff facet_wrap( ~ condition_2) + #facet_grid(condition_1 ~ condition_2) + # alternative to facet_wrap if you have overlapping conditions scale_color_manual('Signficant\nIsoform Switch', values = c('black','red')) + labs(x='dIF', y='-Log10 ( Isoform Switch Q Value )') + theme_bw()

but it generate plot for only 5 condition. Could it plot for more than 5 conditions?