The spectrum of all planetary objects (and humans, for that matter) has a double hump - a one in the visible region due to reflected sunlight and another in the infrared due to thermal emission of the planet.
The Jupiter case:
Here is the "laboratory" set up to show the different types of spectra - continuous, absorption lines and emission lines- 2 versions....
For visible wavelengths think of the Sun as the hot light source and the planet providing the thin cloud of gas. For infrared wavelengths it is the planet that is emitting.
Example of atmospheric absorption spectrum -
To be compared with lab spectra of various potential atmospheric constituents:
Here is an emission spectrum - from Titan's stratosphere:
Here is a fit to the black body spectrum of the IR emission from Earth - there are some absorption features so that the fit is only to the continuum part of the emission spectrum.
From which we conclude that the average black body temperature of the emitting atmosphere (the troposphere) is about 280K. Moreon atmospheric temperatures later....
It's these strong absorption bands in the red part of the visible spectrum that make Uranus and Neptune look blue.
(But what makes Jupiter and Saturn look orange is another story.... later).
N.B. the horizontal axis is Wavenumber = 1/Wavelength.
Humans are like planets - they reflect visible sunlight and emit IR.
It is the clouds that are reflecting sunlight - some of the clouds are colored red-ish. In the IR picture the brighter the light the hotter the gas - and deeper in Jupiter's atmosphere - between the clouds. Note that the Great Red Spot is COOL.
Because planetary atmospheres absorb at specific wavelengths, if you look at planets at different wavelengths you see differnent layers of the atmosphere.
Venus in UV (left) and visible (right). Note how UV light is reflected by high altitude clouds but heavily absorbed (dark) high up in the atmosphere. Visible light is reflected by clouds - higher up and lower down.
"color" Venus in UV - not true color - aagh!
Earth in visible (left) and IR (right) light. Note the tropospheric weather patterns in the IR. In the IR dark = absorption by water vapor in the atmosphere. In the visible dark = absorption by (dark) ocean or land.
Titan in broadband visible light - Voyager (color bit exagerated):
HST and ground-based IR do a little better - with narrow wavebands - peaking at surface in a waveband where the atmosphere is less absorbing.
Titan in IR (red, green) and UV (blue) - Cassini cameras:
Titan at different IR wavelengths - Cassini VIMS
UV absorption in the Earth's atmosphere.
The Ozone Hole
Here is an image of the Earth in UV light - taken by Apollo 16 astronauts from the Moon
And a more recent picture of the Earth taken by the orbiter called IMAGE - this is helium emission (in the EUV) from the escaping He atoms in the outermost regions of the atmosphere - the exosphere.